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Small tetraheme cytochrome c from Shewanella oneidensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 5 mg/mL of purified cytochrome (1 mM HEPES pH 8.0) were mixed with reservoir solution (16 PEG 3350, 15 mM ZnSO4 in 1:1 (v/v) ratio and placed at 277 K in sitting drop vapor diffusion dishes. Crystals were harvested after ca. 10 days and transferred to 30% PEG 400 before freezing in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.21 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.595 α = 90 b = 63.856 β = 97.21 c = 28.979 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 CCD ADSC QUANTUM 315r 2014-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.999999 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.394 16.922 98.8 0.082 0.041 0.997 10.8 4.7 34487
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.47 95.2 0.612 0.31 0.836 3.1 4.5
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 1M1R 1.394 16.922 1.6 34325 3428 98.31 0.1658 0.1639 0.1647 0.1832 0.1829
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 28.157 f_angle_d 1.698 f_chiral_restr 0.089 f_bond_d 0.024 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 669 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 175
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing