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Structure of the mixed-valence, active 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 2VHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 278 30% 5/4 PO/OH and 0.1M MES pH6.0 in the presence of 2mM CaCl2, 10mM sodium ascorbate and 0.2mM FMN, using a 20mg/mL protein solution previously incubated with calcium, sodium ascorbate and FMN.
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.942 α = 90 b = 88.78 β = 90 c = 93.122 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 CMOS BRUKER PHOTON 100 2016-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.5418
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 1.79 64.3 99.1 0.1565 10.3 9.2 61589
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 1.79 1.82 0.8398
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 2VHD 1.8 23.82 57511 2997 98.71 0.20946 0.20769 0.2171 0.2436 0.2492 RANDOM 21.856
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] 0.04 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.62 r_dihedral_angle_4_deg 16.007 r_dihedral_angle_3_deg 13.663 r_dihedral_angle_1_deg 6.167 r_long_range_B_refined 6.167 r_long_range_B_other 6.114 r_scangle_other 4.905 r_scbond_it 3.667 r_scbond_other 3.663 r_mcangle_it 2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.62 r_dihedral_angle_4_deg 16.007 r_dihedral_angle_3_deg 13.663 r_dihedral_angle_1_deg 6.167 r_long_range_B_refined 6.167 r_long_range_B_other 6.114 r_scangle_other 4.905 r_scbond_it 3.667 r_scbond_other 3.663 r_mcangle_it 2.76 r_mcangle_other 2.76 r_angle_refined_deg 2.198 r_mcbond_other 2.119 r_mcbond_it 2.118 r_angle_other_deg 1.228 r_chiral_restr 0.139 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.01 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5062 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement PROTEUM data reduction SAINT data scaling PHASER phasing