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Three dimensional Structure of the Y43L mutant of Tetraheme Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 7.4 277 ethanol, pH 7.4, SMALL TUBES, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.22 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.868 α = 90 b = 67.309 β = 90 c = 34.328 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 MARRESEARCH 2001-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.7 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 0.913 26.343 95.7 0.044 82305 82055 1 2
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) 0.91 0.96 88.1 0.221
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2CDV 0.91 10 1 81910 67354 5786 88.7 0.1078 0.1015 0.0994 0.136 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 2 1019 1393.98
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.105 s_approx_iso_adps 0.094 s_zero_chiral_vol 0.084 s_anti_bump_dis_restr 0.084 s_angle_d 0.053 s_similar_adp_cmpnt 0.052 s_from_restr_planes 0.0316 s_bond_d 0.028 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 802 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 188
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CNS refinement SHELXL-97 refinement CCP4 data scaling CNS phasing