☰ Navigation Tabs
Crystal structure of the Mycobacterium tuberculosis transcriptional repressor EthR2 in complex with BDM41420
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ICI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 200 mM NaCl, 200 mM Na citrate pH 4.2 and 15% polyethylene glycol monomethylether 5000
Crystal Properties Matthews coefficient Solvent content 2.03 39.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.8 α = 90 b = 74.21 β = 90 c = 88.14 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 PIXEL DECTRIS PILATUS3 6M 2013-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979338 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 40 99.8 0.121 0.999 19.21 12.83 15854
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.54 98.8 1.117 0.849 2.81 13.1
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 5ICI 2.4 37.89 15053 793 99.8 0.21422 0.21182 0.2162 0.26015 0.2598 RANDOM 49.358
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] -0.03 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.012 r_dihedral_angle_4_deg 16.247 r_dihedral_angle_3_deg 14.69 r_long_range_B_refined 8.348 r_long_range_B_other 8.346 r_scangle_other 6.535 r_mcangle_it 5.152 r_mcangle_other 5.152 r_dihedral_angle_1_deg 4.966 r_scbond_it 4.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.012 r_dihedral_angle_4_deg 16.247 r_dihedral_angle_3_deg 14.69 r_long_range_B_refined 8.348 r_long_range_B_other 8.346 r_scangle_other 6.535 r_mcangle_it 5.152 r_mcangle_other 5.152 r_dihedral_angle_1_deg 4.966 r_scbond_it 4.393 r_scbond_other 4.392 r_mcbond_it 3.637 r_mcbond_other 3.6 r_angle_refined_deg 1.578 r_angle_other_deg 0.989 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 2783 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction MOLREP phasing XDS data scaling