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Crystal structure of c-type cytochrome XoxG from Methylobacterium extorquens AM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 298 .2 M sodium acetate, 0.1 M phosphate-citra
te pH 4.2, and 20% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.5 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.841 α = 90 b = 95.841 β = 90 c = 80.411 γ = 120
Symmetry Space Group P 62 2 2
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 2018-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.6984 ALS 8.2.2
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 2.71 50 98.6 0.124 0.02 0.999 39 37.7 6337 39.79
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 2.71 2.76 1.242 0.256 0.898
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 2.71 41.5 1.38 6236 313 98.75 0.1963 0.1937 0.1875 0.2484 0.2417 39.79
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 8.4804 f_angle_d 0.9695 f_chiral_restr 0.0465 f_bond_d 0.0073 f_plane_restr 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1252 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHARP phasing