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Crystal structure of the K87V mutant of cytochrome c' from Shewanella benthica DB6705
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6A3K 6A3K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 400 mM sodium phosphate monobasic / 1600 mM potassium phosphate dibasic, 100 mM imidazole / hydrochloric acid pH 8.0, and 200 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.27 45.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.773 α = 90 b = 68.259 β = 112.036 c = 45.507 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS IV++ 2021-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.540
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.06 42.18 99 0.096 0.113 7 3.62 15616
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.06 2.13 97.9 0.466 0.547 1.9 3.61
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6A3K 2.06 37.43 1.36 15580 1549 98.74 0.2072 0.2021 0.2023 0.2545 0.2548 37.3
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.2869 f_angle_d 1.297 f_chiral_restr 0.0782 f_bond_d 0.0132 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1984 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 86
Software Software Software Name Purpose d*TREK data reduction d*TREK data scaling PHENIX refinement PDB_EXTRACT data extraction PHENIX phasing