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Crystal structure of FAD-dependent oxidase CpaO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.32 46.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.245 α = 90 b = 118.245 β = 90 c = 68.891 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 80 PIXEL DECTRIS EIGER X 9M 2022-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.179 30 98.96 0.038 58.19 9 178136
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.179 1.22 0.431 0.148 0.941 5.33
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1.179 24.246 178136 8926 98.959 0.164 0.1635 0.1733 0.1736 0.1865 14.425
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] 0.001 0.001 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.726 r_dihedral_angle_3_deg 11.781 r_dihedral_angle_1_deg 6.246 r_lrange_it 5.593 r_lrange_other 5.161 r_dihedral_angle_2_deg 4.949 r_scangle_other 1.66 r_scangle_it 1.657 r_scbond_other 1.037 r_scbond_it 1.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.726 r_dihedral_angle_3_deg 11.781 r_dihedral_angle_1_deg 6.246 r_lrange_it 5.593 r_lrange_other 5.161 r_dihedral_angle_2_deg 4.949 r_scangle_other 1.66 r_scangle_it 1.657 r_scbond_other 1.037 r_scbond_it 1.036 r_angle_refined_deg 1.017 r_mcangle_it 0.953 r_mcangle_other 0.953 r_angle_other_deg 0.602 r_mcbond_it 0.595 r_mcbond_other 0.594 r_symmetry_nbd_refined 0.31 r_nbd_refined 0.264 r_symmetry_nbd_other 0.248 r_nbd_other 0.247 r_dihedral_angle_other_2_deg 0.219 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.13 r_xyhbond_nbd_refined 0.111 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.05 r_gen_planes_refined 0.013 r_gen_planes_other 0.011 r_bond_refined_d 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3434 Nucleic Acid Atoms Solvent Atoms 697 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection SCALA data scaling MOLREP phasing HKL-2000 data reduction