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ShyA Endopeptidase from Vibrio cholerae (Closed form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GU1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 0.2 M Malonic Acid pH 6.0, 14% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.115 α = 90 b = 87.252 β = 100.37 c = 74.973 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 S 6M 2017-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.97750 CHESS F1
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 2.08 50 99.4 0.119 0.129 0.049 4.3 6.7 46469
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.12 99.3 0.948 6.6
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-Factor (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 THROUGHOUT 2GU1 2.08 49.55 43887 2297 99.38 0.1807 0.1779 0.1854 0.2334 0.2357 RANDOM 27.654
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] 0.12 0.76 -0.08 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.678 r_dihedral_angle_4_deg 18.175 r_dihedral_angle_3_deg 16.849 r_dihedral_angle_1_deg 7.345 r_angle_refined_deg 2.007 r_angle_other_deg 1.394 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.678 r_dihedral_angle_4_deg 18.175 r_dihedral_angle_3_deg 16.849 r_dihedral_angle_1_deg 7.345 r_angle_refined_deg 2.007 r_angle_other_deg 1.394 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5632 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing Coot model building