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Cytochrome c peroxidase YhjA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HQ6 CcpA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.8 M Na/K tartrate
100 mM HEPES/NaOH
2.5 mM Na2S2O4
Crystal Properties Matthews coefficient Solvent content 5.1 76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.42 α = 90 b = 101.42 β = 90 c = 134.68 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 315 2010-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9393 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.57 82 100 0.139 0.037 0.999 17.1 15.4 23032 2 54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.69 100 1.363 0.359 0.785 2.6 15.2
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 FREE R-VALUE 2.572 81.149 22976 1185 99.952 0.175 0.1724 0.2042 0.2219 0.2484 40.199
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] -0.266 -0.266 0.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.428 r_dihedral_angle_6_deg 14.611 r_dihedral_angle_2_deg 7.899 r_dihedral_angle_1_deg 7.175 r_lrange_it 7.125 r_lrange_other 7.081 r_scangle_it 5.775 r_scangle_other 5.638 r_mcangle_it 4.371 r_mcangle_other 4.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.428 r_dihedral_angle_6_deg 14.611 r_dihedral_angle_2_deg 7.899 r_dihedral_angle_1_deg 7.175 r_lrange_it 7.125 r_lrange_other 7.081 r_scangle_it 5.775 r_scangle_other 5.638 r_mcangle_it 4.371 r_mcangle_other 4.371 r_scbond_it 3.752 r_scbond_other 3.648 r_mcbond_it 2.919 r_mcbond_other 2.919 r_angle_refined_deg 1.954 r_angle_other_deg 0.644 r_nbd_refined 0.298 r_symmetry_nbd_other 0.214 r_symmetry_xyhbond_nbd_refined 0.196 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.169 r_nbd_other 0.141 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.085 r_symmetry_nbd_refined 0.077 r_metal_ion_refined 0.071 r_xyhbond_nbd_other 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.01 r_bond_refined_d 0.008 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3268 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing