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Crystal structure of the Arginine Repressor from the pathogenic bacterium Corynebacterium pseudotuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ERE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 100 mM Tris-HCl
200 mM NaCl
10% ethanol
Crystal Properties Matthews coefficient Solvent content 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.191 α = 90 b = 83.191 β = 90 c = 83.191 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 2015-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 48 99.9 0.079 0.999 20.81 10.5 15299 -3 36.141
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.02 99.5 0.899 2.15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ERE 1.9 48 14533 764 99.95 0.1819 0.1797 0.1898 0.2249 0.2245 RANDOM 34.866
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 r_dihedral_angle_2_deg 39.339 r_dihedral_angle_4_deg 20.664 r_dihedral_angle_3_deg 17.714 r_dihedral_angle_1_deg 6.793 r_mcangle_it 3.347 r_mcbond_other 2.415 r_mcbond_it 2.414 r_angle_refined_deg 2.372 r_angle_other_deg 1.157 r_chiral_restr 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.339 r_dihedral_angle_4_deg 20.664 r_dihedral_angle_3_deg 17.714 r_dihedral_angle_1_deg 6.793 r_mcangle_it 3.347 r_mcbond_other 2.415 r_mcbond_it 2.414 r_angle_refined_deg 2.372 r_angle_other_deg 1.157 r_chiral_restr 0.145 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1158 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 31
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing