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Cytochrome c peroxidase with bound guaiacol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V23 PDB ENTRY 2V23
Crystallization Crystal Properties Matthews coefficient Solvent content 3.03 59.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.106 α = 90 b = 74.99 β = 90 c = 106.903 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 IMAGE PLATE RIGAKU-MSC R-AXIS 4 MULTILAYER 2006-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
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 1.61 27.2 85.1 0.03 30.8 4.2 46241
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 1.61 1.69 25.9 0.14 5.6 1.35
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 PDB ENTRY 2V23 1.61 27.24 43821 2369 85.69 0.17892 0.17727 0.1712 0.20953 0.2014 RANDOM 13.973
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.172 r_dihedral_angle_4_deg 22.42 r_dihedral_angle_3_deg 11.358 r_dihedral_angle_1_deg 5.239 r_scangle_it 3.094 r_scbond_it 2.122 r_mcangle_it 1.348 r_angle_refined_deg 1.127 r_mcbond_it 0.853 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.172 r_dihedral_angle_4_deg 22.42 r_dihedral_angle_3_deg 11.358 r_dihedral_angle_1_deg 5.239 r_scangle_it 3.094 r_scbond_it 2.122 r_mcangle_it 1.348 r_angle_refined_deg 1.127 r_mcbond_it 0.853 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.198 r_symmetry_hbond_refined 0.092 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2342 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling