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KstR, transcriptional repressor of cholesterol degradation in Mycobacterium tuberculosis, bound to the DNA operator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MNL PDB ENTRY 3MNL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.1 0.2 M SODIUM SULFATE, 8% TACSIMATE, PH 5.1; 21.7% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.4 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.53 α = 90 b = 62.781 β = 89.9 c = 98.647 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC CCD MIRRORS 2015-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 2.26 49.51 87.3 0.06 8.9 2.4 20253 0.5 41.9
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 2.26 2.38 50.1 0.25 1.7 1.7
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 PDB ENTRY 3MNL 2.26 44.31 19214 1036 87.12 0.20539 0.20182 0.2078 0.27039 0.2702 RANDOM 33.149
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] -3.03 0.56 3.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.707 r_dihedral_angle_4_deg 19.585 r_dihedral_angle_3_deg 18.037 r_dihedral_angle_1_deg 5.191 r_mcangle_it 3.483 r_scbond_it 2.651 r_mcbond_it 2.218 r_mcbond_other 2.216 r_angle_refined_deg 1.484 r_angle_other_deg 0.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.707 r_dihedral_angle_4_deg 19.585 r_dihedral_angle_3_deg 18.037 r_dihedral_angle_1_deg 5.191 r_mcangle_it 3.483 r_scbond_it 2.651 r_mcbond_it 2.218 r_mcbond_other 2.216 r_angle_refined_deg 1.484 r_angle_other_deg 0.964 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2797 Nucleic Acid Atoms 650 Solvent Atoms 96 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing