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ShyA endopeptidase from Vibrio cholera (open form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GUI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 Protein (0.5 microliter): 18 mg/ml in 20 mM Tris-HCl, 150 mM NaCl pH 7.6
Precipitant (0.5 microliter): 0.25 M sodium citrate, 10% polyethylene glycol 3350, 0.1 M Tris-HCl pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.74 59.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.272 α = 90 b = 82.492 β = 102.692 c = 82.522 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 125 PIXEL DECTRIS EIGER X 9M 2018-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07811 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.025 54.9 54.1 0.055 0.059 0.011 0.998 9.8 7 17391 60.31
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 2.026 2.276 66.7 1.13 1.234 0.487 0.549 1.6 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2GUI 2.3 36.58 16347 842 74.4 0.2538 0.255 0.2936 0.2911 Random 78.09
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.736 f_angle_d 0.635 f_chiral_restr 0.0473 f_bond_d 0.0034 f_plane_restr 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2852 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement PHASER phasing PDB_EXTRACT data extraction STARANISO data scaling autoPROC data scaling XDS data reduction