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The structure of apo-SoBcmB with Fe(II) and AKG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 7V3O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1M Potassium chloride, 0.1M HEPES pH 7, 1M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.63 53.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.677 α = 90 b = 101.677 β = 90 c = 130.922 γ = 120
Symmetry Space Group P 61 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 PIXEL DECTRIS PILATUS 6M 2020-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9792 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.2 44.03 100 0.111 0.115 0.032 0.998 17.2 12 20954 25.061
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 100 0.942 0.979 0.264 0.873 5.1 13.8
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.2000308002 26.7825539092 1.33484361805 20887 1108 99.9664975591 0.188791274986 0.186932196069 0.189 0.221102034271 0.2224 39.0559365877
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 9.35782566706 f_angle_d 0.937461009432 f_chiral_restr 0.05497845187 f_bond_d 0.00852602520632 f_plane_restr 0.00570997425822
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2135 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction pointless data scaling PHASER phasing