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Electron transfer complexes: Experimental mapping of the redox-dependent cytochrome c electrostatic surface
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HRC PDB ENTRY 1HRC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 300 High concentration of NaNO3 and 10% Ditionite in the wells, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.695 α = 90 b = 79.695 β = 90 c = 89.247 γ = 120
Symmetry Space Group P 31 2 1
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 OXFORD ONYX CCD 2008-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 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 1.75 69.01 95.3 0.116 9 2.9 31828
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 1.75 1.81 95.1 95.1 0.43 2.5 2.9
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 PDB ENTRY 1HRC 1.75 69.01 31828 1697 99.94 0.18863 0.18558 0.1842 0.24761 0.2433 RANDOM 17.894
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] -0.3 -0.15 -0.3 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.338 r_dihedral_angle_4_deg 25.189 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_1_deg 6.159 r_scangle_it 3.975 r_scbond_it 2.591 r_angle_refined_deg 1.742 r_mcangle_it 1.6 r_mcbond_it 1.104 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.338 r_dihedral_angle_4_deg 25.189 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_1_deg 6.159 r_scangle_it 3.975 r_scbond_it 2.591 r_angle_refined_deg 1.742 r_mcangle_it 1.6 r_mcbond_it 1.104 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.271 r_symmetry_hbond_refined 0.227 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.109 r_bond_refined_d 0.021 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2478 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 217
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling