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Structure of Atopobium parvulum SufS C375S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J8Q PDB entry 5J8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 22% PEG3350, 50 mM sodium malate
Crystal Properties Matthews coefficient Solvent content 2.56 51.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.12 α = 90 b = 110.612 β = 90 c = 122.343 γ = 90
Symmetry Space Group P 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2019-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 29.8 97.2 0.99 17.1 2.9 47832 27.31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 0.955 3.9
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 PDB entry 5J8Q 2.2 29.8 1.34 47798 2893 72.6 0.1971 0.1952 0.1959 0.2413 0.2406 30.19
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 5.6669 f_angle_d 0.5567 f_chiral_restr 0.0431 f_plane_restr 0.004 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6135 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement d*TREK data scaling PDB_EXTRACT data extraction d*TREK data reduction PHASER phasing Coot model building