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High-resolution three-dimensional structure of horse heart cytochrome C at room temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HRC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 1.0-1.5M sodium chloride, 2.7-3.2M ammonium sulfate, 0.1M sodium phosphate
Crystal Properties Matthews coefficient Solvent content 3.06 59.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.395 α = 90 b = 58.395 β = 90 c = 41.909 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD RIGAKU SATURN 944+ 2016-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.8 23.9569 99.9 0.05 16.6 3.48 13227
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 1.8 1.86 99.9 0.347
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 FREE R-VALUE 1HRC 1.8 19.72 12588 626 99.86 0.1678 0.1663 0.1769 0.1987 0.2156 RANDOM SELECTON 36.311
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.03 r_dihedral_angle_3_deg 16.822 r_long_range_B_refined 9.733 r_long_range_B_other 9.731 r_scangle_other 8.272 r_dihedral_angle_1_deg 7.719 r_dihedral_angle_4_deg 6.884 r_scbond_other 5.266 r_scbond_it 5.257 r_mcangle_it 3.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.03 r_dihedral_angle_3_deg 16.822 r_long_range_B_refined 9.733 r_long_range_B_other 9.731 r_scangle_other 8.272 r_dihedral_angle_1_deg 7.719 r_dihedral_angle_4_deg 6.884 r_scbond_other 5.266 r_scbond_it 5.257 r_mcangle_it 3.848 r_mcangle_other 3.846 r_mcbond_it 2.825 r_mcbond_other 2.817 r_angle_refined_deg 1.818 r_angle_other_deg 1.449 r_chiral_restr 0.081 r_gen_planes_refined 0.014 r_bond_refined_d 0.013 r_gen_planes_other 0.012 r_bond_other_d 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 826 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling MOLREP phasing