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Crystal structure of the PadR-family transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv in complex with cadmium 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 4.6 296 0.1 M sodium acetate, 2.0 M sodium formate
Crystal Properties Matthews coefficient Solvent content 1.96 37.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.496 α = 90 b = 49.291 β = 90 c = 127.338 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++ 2016-06-11 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) R Merge I (Observed) 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 63.67 95.6 0.12 19.17 10.1 9947
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 2.2 2.28 0.52 2.32
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ZHC 2.2 63.67 9457 464 95.73 0.19338 0.1912 0.23999 0.2036 RANDOM 32.66
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] -1.84 1.78 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.703 r_dihedral_angle_4_deg 21.574 r_dihedral_angle_3_deg 15.351 r_dihedral_angle_1_deg 6.443 r_long_range_B_refined 5.026 r_long_range_B_other 5.005 r_scangle_other 3.589 r_mcangle_other 2.466 r_mcangle_it 2.465 r_scbond_it 2.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.703 r_dihedral_angle_4_deg 21.574 r_dihedral_angle_3_deg 15.351 r_dihedral_angle_1_deg 6.443 r_long_range_B_refined 5.026 r_long_range_B_other 5.005 r_scangle_other 3.589 r_mcangle_other 2.466 r_mcangle_it 2.465 r_scbond_it 2.138 r_scbond_other 2.132 r_angle_refined_deg 1.81 r_mcbond_it 1.529 r_mcbond_other 1.526 r_angle_other_deg 1.016 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1648 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing