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Crystal structure of Arginine Repressor P115Q mutant from the pathogenic bacterium Corynebacterium pseudotuberculosis bound to arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 2.0 M Sodium Formate, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.69 54.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.341 α = 90 b = 83.341 β = 90 c = 83.341 γ = 90
Symmetry Space Group P 21 3
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 2M 2017-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4586 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.7 37.271 99.9 0.055 0.056 1 48.98 35.1 21469 40.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 99.5 2.587 2.656 0.369 1.15 19.4
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 THROUGHOUT 5JVO 1.701 37.271 14.16 21457 1073 99.95 0.1805 0.1733 0.1845 0.1972 0.2026 36.8252
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 10.01 f_angle_d 0.936 f_chiral_restr 0.048 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1211 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 42
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction