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Mycobacterium tuberculosis transcriptional regulator EthR with bound inhibitory compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 300 PEG based
Crystal Properties Matthews coefficient Solvent content 2.6 52.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.164 α = 90 b = 121.164 β = 90 c = 33.693 γ = 90
Symmetry Space Group P 41 21 2
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 6M 2018-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.53 54.09 100 0.999 16.4 12.5 20672
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 1.89 1.94 0.735 2
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 5NIO 1.89 42.87 19571 1056 99.86 0.2001 0.1988 0.2224 0.2212 RANDOM 30.949
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] 1.55 1.55 -3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.791 r_dihedral_angle_4_deg 17.283 r_dihedral_angle_3_deg 13.78 r_dihedral_angle_1_deg 5.729 r_mcangle_it 3.921 r_mcbond_it 2.834 r_mcbond_other 2.828 r_angle_other_deg 2.328 r_angle_refined_deg 1.757 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.791 r_dihedral_angle_4_deg 17.283 r_dihedral_angle_3_deg 13.78 r_dihedral_angle_1_deg 5.729 r_mcangle_it 3.921 r_mcbond_it 2.834 r_mcbond_other 2.828 r_angle_other_deg 2.328 r_angle_refined_deg 1.757 r_chiral_restr 0.102 r_gen_planes_other 0.039 r_bond_other_d 0.035 r_gen_planes_refined 0.018 r_bond_refined_d 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1499 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling pointless data reduction PHASER phasing