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Crystal structure of the PadR-family transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv in complex with Manganese ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 294 0.1M Sodium Acetate pH 4.6,
2M Sodium Formate
Crystal Properties Matthews coefficient Solvent content 1.97 37.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.491 α = 90 b = 47.899 β = 90 c = 129.878 γ = 90
Symmetry Space Group P 21 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++ 2019-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 2.8 26.89 99.9 0.996 9.7 6.6 5103
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 2.8 2.95 0.996
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 5ZHC 2.8 26.89 4484 587 99.78 0.2271 0.2207 0.2203 0.272 0.2714 RANDOM 49.609
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] -3.52 9.92 -6.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.19 r_dihedral_angle_3_deg 21.362 r_dihedral_angle_4_deg 18.796 r_dihedral_angle_1_deg 5.598 r_angle_refined_deg 1.019 r_chiral_restr 0.089 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1552 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing