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CRYSTAL STRUCTURE OF THE DI-HAEM CYTOCHROME C PEROXIDASE FROM PARACOCCUS PANTOTROPHUS - Mixed VALENCE FORM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E7B PDB ENTRY 1E7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.9 ECHALER ET AL., (2004). ACTA CRYST. D60, 331-333, pH 7.90
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.37 α = 90 b = 141.2 β = 90 c = 51.58 γ = 90
Symmetry Space Group P 21 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 CCD MIRRORS 2003-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.2 49 93 0.07 23 6.7 212598 -3
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 1.2 1.24 84 0.57 1.7 4.3
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1E7B 1.2 48.22 203984 8614 92.5 0.174 0.173 0.188 RANDOM 18.64
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] 0.14 0.03 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.121 r_dihedral_angle_4_deg 15.088 r_dihedral_angle_3_deg 12.646 r_dihedral_angle_1_deg 5.473 r_scangle_it 3.379 r_scbond_it 2.232 r_angle_refined_deg 1.557 r_mcangle_it 1.517 r_mcbond_it 1.027 r_nbd_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.121 r_dihedral_angle_4_deg 15.088 r_dihedral_angle_3_deg 12.646 r_dihedral_angle_1_deg 5.473 r_scangle_it 3.379 r_scbond_it 2.232 r_angle_refined_deg 1.557 r_mcangle_it 1.517 r_mcbond_it 1.027 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.165 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.096 r_metal_ion_refined 0.06 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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_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 5056 Nucleic Acid Atoms Solvent Atoms 1055 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing