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Cytochrome c Peroxidase BccP of Shewanella oneidensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HQ6 pdb entry 3HQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 298 reduced with sodium dithionite, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.84 α = 113.96 b = 81.22 β = 102.1 c = 85.92 γ = 90.01
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 IMAGE PLATE MAR scanner 300 mm plate 2009-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.93 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 40.5 93.7 0.08 0.113 6.7 1.9 200196 106139 10.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3HQ6 1.8 40.5 200196 100779 5345 93.68 0.20055 0.19759 0.2094 0.25695 0.2662 RANDOM 21.729
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 0.01 0.04 -0.05 0.01 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.833 r_dihedral_angle_3_deg 14.672 r_dihedral_angle_4_deg 9.193 r_dihedral_angle_1_deg 5.814 r_scangle_it 1.9 r_scbond_it 1.274 r_angle_refined_deg 1.232 r_angle_other_deg 0.892 r_mcangle_it 0.71 r_mcbond_it 0.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.833 r_dihedral_angle_3_deg 14.672 r_dihedral_angle_4_deg 9.193 r_dihedral_angle_1_deg 5.814 r_scangle_it 1.9 r_scbond_it 1.274 r_angle_refined_deg 1.232 r_angle_other_deg 0.892 r_mcangle_it 0.71 r_mcbond_it 0.421 r_mcbond_other 0.113 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9419 Nucleic Acid Atoms Solvent Atoms 1308 Heterogen Atoms 354
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling