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The structure of oxidized rat cytochrome c at 1.13 angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZOO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 PEG 4000, isopropanol, sodium acetate, potassium ferricyanate
Crystal Properties Matthews coefficient Solvent content 2.24 45.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.401 α = 110.04 b = 52.471 β = 92.77 c = 61.647 γ = 92.02
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 MARMOSAIC 225 mm CCD 2014-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.1236 49.22 87.4 0.05 14.4 3.9 134553 127840
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 1.1236 1.153 44.66 0.548 2 3.7
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 3ZOO 1.1236 49.22 127840 6713 87.4 0.13321 0.13184 0.132 0.15928 0.1598 RANDOM 15.968
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] 0.75 -0.17 0.45 -0.24 0.31 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.761 r_sphericity_free 31.971 r_dihedral_angle_4_deg 31.488 r_dihedral_angle_3_deg 11.439 r_sphericity_bonded 10.542 r_dihedral_angle_1_deg 6.732 r_long_range_B_refined 3.493 r_long_range_B_other 2.77 r_rigid_bond_restr 2.513 r_angle_refined_deg 1.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.761 r_sphericity_free 31.971 r_dihedral_angle_4_deg 31.488 r_dihedral_angle_3_deg 11.439 r_sphericity_bonded 10.542 r_dihedral_angle_1_deg 6.732 r_long_range_B_refined 3.493 r_long_range_B_other 2.77 r_rigid_bond_restr 2.513 r_angle_refined_deg 1.903 r_scangle_other 1.854 r_scbond_it 1.547 r_scbond_other 1.542 r_mcangle_it 1.378 r_mcangle_other 1.378 r_angle_other_deg 1.182 r_mcbond_it 1.08 r_mcbond_other 1.079 r_chiral_restr 0.124 r_gen_planes_refined 0.018 r_bond_refined_d 0.017 r_gen_planes_other 0.016 r_bond_other_d 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3228 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement PHENIX refinement Aimless data scaling PHENIX phasing