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W96Y Oxalate Decarboxylase (Bacillus subtilis)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TZP PDB entry 6TZP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 7% PEG8000, 100 mM Tris, 200 mM magnesium chloride, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.3 62.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.27 α = 90 b = 155.27 β = 90 c = 124.088 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2017-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.717 32.447 99.82 0.08886 0.02205 0.99 30.6 22.2 1351073 60978
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.782 98.51 0.3797 9.43 21.2 126689
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 PDB entry 6TZP 1.72 32.447 1.36 60977 3115 99.76 0.1497 0.149 0.1491 0.1661 0.1663 14.5526
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 14.931 f_angle_d 0.885 f_chiral_restr 0.061 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3011 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing