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Mixed-valence, active form, of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae at 1.4 Angstrom resolution
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 278 0.1 M MES pH 6.0, 30 % 5/4 PO/OH, 2 mM CaCl2, 10 mM sodium ascorbate and 0.2 mM FMN
Crystal Properties Matthews coefficient Solvent content 2.1 43.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.842 α = 90 b = 89.144 β = 90 c = 89.731 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 100 PIXEL DECTRIS PILATUS 2M-F 2016-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 39.95 99.9 0.068 0.999 11.4 6.4 124619
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 0.0656 0.813
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 1.4 39.95 118011 6220 99.6 0.19763 0.19638 0.2059 0.22096 0.2272 RANDOM 18.815
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] -0.22 -1.55 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.305 r_dihedral_angle_4_deg 19.409 r_dihedral_angle_3_deg 11.688 r_dihedral_angle_1_deg 5.726 r_long_range_B_refined 4.92 r_long_range_B_other 4.864 r_scangle_other 4.261 r_scbond_other 3.028 r_scbond_it 3.027 r_mcangle_it 2.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.305 r_dihedral_angle_4_deg 19.409 r_dihedral_angle_3_deg 11.688 r_dihedral_angle_1_deg 5.726 r_long_range_B_refined 4.92 r_long_range_B_other 4.864 r_scangle_other 4.261 r_scbond_other 3.028 r_scbond_it 3.027 r_mcangle_it 2.322 r_mcangle_other 2.322 r_angle_refined_deg 1.972 r_mcbond_it 1.784 r_mcbond_other 1.781 r_angle_other_deg 1.193 r_chiral_restr 0.126 r_bond_refined_d 0.012 r_gen_planes_other 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5050 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing