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Caspases from Scleractinian Coral
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J30
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291 Protein crystalized in a solution of 0.1 M sodium malonate pH 5.0,
12% w/v polyethylene glycol (PEG) 3350, and conditions were optimized
such that the best diffracting crystals of PaCasp7a were obtained at
18 C in a solution of 0.1 M sodium malonate, pH 4.9-5.1, 15-17%
PEG 3350 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals for PaCasp7a appeared
within 3 to 5 days and were briefly immersed in a cryogenic solution
containing 20% PEG 4000, 80% reservoir solution
Crystal Properties Matthews coefficient Solvent content 2.73 54.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.416 α = 90 b = 86.848 β = 90 c = 93.666 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2018-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.57 50 98.8 0.218 0.249 0.117 9 4.9 84182
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.6 99.5 1.461 1.642 0.733 0.255 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2J30 1.57 39.4 1.33 83910 1990 98.48 0.178 0.1772 0.178 0.209 0.2094 17.6375
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3843 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms 1547
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction DENZO data reduction PHENIX phasing