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Structure of the azide-inhibited form of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 30 % 5/4 PO/OH and 0.1 M MES pH 6.0 in the presence of 2 mM CaCl2, 10 mM sodium ascorbate and 0.2 mM FMN
Crystal Properties Matthews coefficient Solvent content 2.3 46.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.12 α = 90 b = 89.14 β = 90 c = 94.83 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 110 PIXEL DECTRIS PILATUS 2M 2016-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 65 97.7 0.117 9.2 5.6 30270
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 2.3 2.38 0.723
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 6FU3 2.3 64.95 28748 1466 99.18 0.17336 0.1712 0.1805 0.21461 0.2212 RANDOM 39.118
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] 0.39 -1.5 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.888 r_dihedral_angle_4_deg 15.076 r_dihedral_angle_3_deg 13.779 r_dihedral_angle_1_deg 6.05 r_long_range_B_refined 4.952 r_long_range_B_other 4.934 r_scangle_other 3.227 r_scbond_it 2.315 r_mcangle_it 2.304 r_mcangle_other 2.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.888 r_dihedral_angle_4_deg 15.076 r_dihedral_angle_3_deg 13.779 r_dihedral_angle_1_deg 6.05 r_long_range_B_refined 4.952 r_long_range_B_other 4.934 r_scangle_other 3.227 r_scbond_it 2.315 r_mcangle_it 2.304 r_mcangle_other 2.304 r_scbond_other 2.197 r_angle_refined_deg 1.907 r_mcbond_it 1.515 r_mcbond_other 1.501 r_angle_other_deg 1.106 r_chiral_restr 0.108 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5059 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction Aimless data scaling PHASER phasing