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Cytochrome c peroxidase from G. sulfurreducens, wild type
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EB7 PDB ENTRY 1EB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 16 % PEG 10000
0.1 M HEPES/NaOH, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.241 α = 68.69 b = 55.783 β = 71.84 c = 78.644 γ = 57.76
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 MAR CCD 165 mm mirrors 2007-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.05 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 70 96.4 0.09 7.9 3 48428 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.1 97.7 0.285 0.285 3 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1EB7 2 70 2 48428 43589 2319 94.64 0.19309 0.18909 0.1918 0.26606 0.2701 RANDOM 24.014
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] 0.44 -2.55 0.77 2.8 -0.71 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.148 r_dihedral_angle_3_deg 18.769 r_dihedral_angle_4_deg 15.383 r_dihedral_angle_1_deg 7.539 r_scangle_it 4.745 r_scbond_it 3.419 r_angle_refined_deg 2.221 r_mcangle_it 2.049 r_mcbond_it 1.366 r_symmetry_hbond_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.148 r_dihedral_angle_3_deg 18.769 r_dihedral_angle_4_deg 15.383 r_dihedral_angle_1_deg 7.539 r_scangle_it 4.745 r_scbond_it 3.419 r_angle_refined_deg 2.221 r_mcangle_it 2.049 r_mcbond_it 1.366 r_symmetry_hbond_refined 0.332 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.256 r_xyhbond_nbd_refined 0.21 r_chiral_restr 0.142 r_metal_ion_refined 0.08 r_bond_refined_d 0.028 r_gen_planes_refined 0.011 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4821 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 174
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling