Crystal Forms

This is a table of constructs of SGC targets (past and present) that have produced crystals of sufficient diffraction quality to allow at least an initial phased model to be produced. A further filter is that all the targets in this table are found in the PDB in some form or another (either deposited by us or others): there are no novel targets to be found here. Furthermore, these models may have been further refined and deposited in the PDB or the project halted for some reason (scooped, insufficient data quality, boredom); the data is provided as is!

This table is primarily an aid for finding:

  • Alternative constructs of a target - maybe better yields, an alternative expression system or more reproducible crystals?
  • Getting different crystallization conditions – no more mounting in the cold room with a RT crystallizing construct or perhaps a more suitable condition for soaking in that compound
  • Alternative crystal forms of a target – avoiding that binding site packing contact and getting a more biologically relevant structure

The model table can be searched using a targets id.

Description of columns

  • (SGC)Model id – self-explanatory. We reiterate that we do not intend to make these models publicly available as they may be misrepresentative or otherwise incorrect
  • Model spacegroup - the model’s indexed space group (maybe incorrect if the final model was not deposited)
  • Model comments - an optional field that may contain comments on how the refiner was feeling that day
  • XDS resolution - the resolution of the scaled data (again maybe incorrect for un-deposited structures)
  • XTBM condition - ingredients of the condition in which crystals of this construct were obtained; probably a good starting point for reproducing this experiment (if it was reproducible)
  • Xtal Plate Protein Concentration – the concentration of the protein stock used to set up the crystallization experiment
  • ConstructID – an SGC identifier, many SGC construct are readily available through  Addgene
  • Construct protein sequence – the full length sequence including any purification tags and protease cleavage sites
  • Expected Mass – the MW of the protein in Daltons
  • Construct protein sequence (no tag) – the sequence of the construct after tag cleavage and removal, PurProt Sequence Cleaved? tells you if it’s relevant (see below)
  • Expected Mass (no tag) – the MW of the cleaved protein in Daltons
  • PurProt Buffer – Contents of the buffer used to store the final purified protein
  • PurProt Buffer pH – pH of the PurProt buffer
  • PurProt Sequence Cleaved? – Yes (yes it was cleaved), No (no it wasn’t cleaved)
  • MS Comments – any discrepancies in weight will be noted here
  • MS 1st Component MW – the weight in Daltons of the main species found in the mass spec experiment
  • Vector Name – the SGC vector used to express and purify the protein, most of these are available through Addgene
  • Vector Protease – if there was a tag and it was cleaved off, this was the protease used
  • Vector Antibiotics – the resistance cassette on the vector backbone
  • Cell Line – the strain of E.coli, insect cells, mammalian cells, etc. used to produce the protein
  • Target ID – the gene name or synonym of the target, either are searchable
  • Domain ID – the PFAM family id code (PFxxxxx)
  • Domain Description – the PFAM family name

As stated above many of these constructs and vectors are available through Addgene: https://www.addgene.org/search/advanced/?q=SGC

The MPCD: Marseille Protein Crystallization Database is similarly searchable protein crystallization database available at: http://www.cinam.univ-mrs.fr/mpcd/

Described in: Acta Cryst. (2006). D62, 1311-1318, https://doi.org/10.1107/S0907444906027594

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XLS
Model Id Model Spacegroup Model Comments XDS Resolution (Scaled) XTBM Condition Xtal Plate Protein Concentration (mg/ml) Purification Protocol Construct ID Construct Protein Sequence Expected Mass Construct Protein Sequence (no tag) Expected Mass (no tag) PurProt Buffer PurProt Buffer PH PurProt Sequence Cleaved? MS Commentssort descending MS 1st Component MW Vector Name Vector Protease Vector Antibiotics Cell Line Target ID Domain ID Domain Description Public Name
JMJD2DA-m120 P 42 21 2 crystal contact - symmetry axis 1.50 0.1M HEPES pH 7.0 -- 0.15M ammonium sulfate -- 25% PEG3350 19.00 Protocol.pdf JMJD2DA-c105 MHHHHHHSSGVDLGTENLYFQSMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 41991.70 SMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 39526.00 20 mM HEPES, 0.5M NaCl, 5% glycerol, 0.5uM TCEP 7.50 yes correct 39527.00 pNIC28-Bsa4 TEV protease Kanamycin BL21(DE3)-R3 JMJD2DA JmjC,JmjN
JMJD2DA-m069 P 43 21 2 peptide site 1.50 0.1M HEPES pH 7.0 -- 0.15M ammonium sulfate -- 25% PEG3350 19.00 Protocol.pdf JMJD2DA-c105 MHHHHHHSSGVDLGTENLYFQSMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 41991.70 SMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 39526.00 20 mM HEPES, 0.5M NaCl, 5% glycerol, 0.5uM TCEP 7.50 yes correct 39527.00 pNIC28-Bsa4 TEV protease Kanamycin BL21(DE3)-R3 JMJD2DA JmjC,JmjN
JMJD2DA-m121 P 42 21 2 crystal contact - hydrotope - p-toluene sulfonate 1.50 0.1M HEPES pH 7.0 -- 0.15M ammonium sulfate -- 25% PEG3350 19.00 Protocol.pdf JMJD2DA-c105 MHHHHHHSSGVDLGTENLYFQSMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 41991.70 SMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 39526.00 20 mM HEPES, 0.5M NaCl, 5% glycerol, 0.5uM TCEP 7.50 yes correct 39527.00 pNIC28-Bsa4 TEV protease Kanamycin BL21(DE3)-R3 JMJD2DA JmjC,JmjN
JMJD2DA-m070 P 43 21 2 crystal contact - ligand hydrolised - covalent with CYS168 1.50 0.1M HEPES pH 7.0 -- 0.15M ammonium sulfate -- 25% PEG3350 19.00 Protocol.pdf JMJD2DA-c105 MHHHHHHSSGVDLGTENLYFQSMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 41991.70 SMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 39526.00 20 mM HEPES, 0.5M NaCl, 5% glycerol, 0.5uM TCEP 7.50 yes correct 39527.00 pNIC28-Bsa4 TEV protease Kanamycin BL21(DE3)-R3 JMJD2DA JmjC,JmjN
JMJD2DA-m122 P 42 21 2 crystal contact - symmetry axis 1.50 0.1M HEPES pH 7.0 -- 0.15M ammonium sulfate -- 25% PEG3350 19.00 Protocol.pdf JMJD2DA-c105 MHHHHHHSSGVDLGTENLYFQSMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 41991.70 SMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 39526.00 20 mM HEPES, 0.5M NaCl, 5% glycerol, 0.5uM TCEP 7.50 yes correct 39527.00 pNIC28-Bsa4 TEV protease Kanamycin BL21(DE3)-R3 JMJD2DA JmjC,JmjN
JMJD2DA-m071 P 43 21 2 allosteric site 1.50 0.1M HEPES pH 7.0 -- 0.15M ammonium sulfate -- 25% PEG3350 19.00 Protocol.pdf JMJD2DA-c105 MHHHHHHSSGVDLGTENLYFQSMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 41991.70 SMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 39526.00 20 mM HEPES, 0.5M NaCl, 5% glycerol, 0.5uM TCEP 7.50 yes correct 39527.00 pNIC28-Bsa4 TEV protease Kanamycin BL21(DE3)-R3 JMJD2DA JmjC,JmjN
JMJD2DA-m123 P 42 21 2 crystal contact 1.50 0.1M HEPES pH 7.0 -- 0.15M ammonium sulfate -- 25% PEG3350 19.00 Protocol.pdf JMJD2DA-c105 MHHHHHHSSGVDLGTENLYFQSMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 41991.70 SMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 39526.00 20 mM HEPES, 0.5M NaCl, 5% glycerol, 0.5uM TCEP 7.50 yes correct 39527.00 pNIC28-Bsa4 TEV protease Kanamycin BL21(DE3)-R3 JMJD2DA JmjC,JmjN
JMJD2DA-m111 P 42 21 2 active site - dubious - good in Patrick's map, not spotted by Pandda 1.50 0.1M HEPES pH 7.0 -- 0.15M ammonium sulfate -- 25% PEG3350 19.00 Protocol.pdf JMJD2DA-c105 MHHHHHHSSGVDLGTENLYFQSMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 41991.70 SMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 39526.00 20 mM HEPES, 0.5M NaCl, 5% glycerol, 0.5uM TCEP 7.50 yes correct 39527.00 pNIC28-Bsa4 TEV protease Kanamycin BL21(DE3)-R3 JMJD2DA JmjC,JmjN
JMJD2DA-m124 P 42 21 2 allosteric pocket - covalent 1.50 0.1M HEPES pH 7.0 -- 0.15M ammonium sulfate -- 25% PEG3350 19.00 Protocol.pdf JMJD2DA-c105 MHHHHHHSSGVDLGTENLYFQSMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 41991.70 SMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 39526.00 20 mM HEPES, 0.5M NaCl, 5% glycerol, 0.5uM TCEP 7.50 yes correct 39527.00 pNIC28-Bsa4 TEV protease Kanamycin BL21(DE3)-R3 JMJD2DA JmjC,JmjN
JMJD2DA-m112 P 42 21 2 crystal contact - hydrolysed - covalent 1.50 0.1M HEPES pH 7.0 -- 0.15M ammonium sulfate -- 25% PEG3350 19.00 Protocol.pdf JMJD2DA-c105 MHHHHHHSSGVDLGTENLYFQSMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 41991.70 SMETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR 39526.00 20 mM HEPES, 0.5M NaCl, 5% glycerol, 0.5uM TCEP 7.50 yes correct 39527.00 pNIC28-Bsa4 TEV protease Kanamycin BL21(DE3)-R3 JMJD2DA JmjC,JmjN
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