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Crystal structure of the PadR-family transcriptional regulator Rv3488 of Mycobacterium tuberculosis H37Rv
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EJO
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 2.01 35.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.633 α = 90 b = 49.099 β = 90 c = 127.325 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++ 2017-03-02 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) Rrim I (All) Rpim I (All) 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 1.97 63.66 99.8 0.075 0.079 0.023 34.06 10.9 14217 31.7
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 1.97 2.01 98.4 0.65 0.7 0.25 0.89 2.06 6.8
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 4EJO 1.97 63.66 13466 703 99.46 0.18766 0.18509 0.1935 0.23773 0.2441 RANDOM 33.427
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] -0.19 1.38 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.57 r_dihedral_angle_4_deg 17.122 r_dihedral_angle_3_deg 13.79 r_dihedral_angle_1_deg 5.201 r_long_range_B_refined 4.673 r_long_range_B_other 4.673 r_scangle_other 2.076 r_angle_refined_deg 1.579 r_mcangle_it 1.478 r_mcangle_other 1.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.57 r_dihedral_angle_4_deg 17.122 r_dihedral_angle_3_deg 13.79 r_dihedral_angle_1_deg 5.201 r_long_range_B_refined 4.673 r_long_range_B_other 4.673 r_scangle_other 2.076 r_angle_refined_deg 1.579 r_mcangle_it 1.478 r_mcangle_other 1.478 r_scbond_it 1.237 r_scbond_other 1.236 r_angle_other_deg 1.001 r_mcbond_it 0.922 r_mcbond_other 0.917 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 1614 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing