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Crystal structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris (Miyazaki F) in the presence of zinc ion
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 294 PEG 6000, zinc acetate, pH 6.5, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.03 59.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.09 α = 90 b = 84.07 β = 90 c = 142.67 γ = 90
Symmetry Space Group P 21 21 21
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 2000-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.7000 SPring-8 BL44B2
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 2.7 30 0.053 13.3 4.72 20426 20426 33.6
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) 2.7 2.8 67.6 0.115 3.6 1369
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.7 27.2 18096 18096 2006 99.5 0.204 0.204 0.198 0.259 0.2514 RANDOM 40.5
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] -3.38 -2.45 5.83
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17 c_scangle_it 6.13 c_mcangle_it 4.66 c_scbond_it 4.6 c_mcbond_it 2.95 c_angle_deg 0.9 c_improper_angle_d 0.64 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 17 c_scangle_it 6.13 c_mcangle_it 4.66 c_scbond_it 4.6 c_mcbond_it 2.95 c_angle_deg 0.9 c_improper_angle_d 0.64 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3813 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 696
Software Software Software Name Purpose CNS refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling CNS phasing