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Mycobacterium tuberculosis DprE1 in complex with inhibitor TCA020
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KW5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.2 M imidazole, 30 - 35% (v/v) polypropyleneglycol 400
Crystal Properties Matthews coefficient Solvent content 2.49 50.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.05 α = 90 b = 84.32 β = 103.67 c = 81.17 γ = 90
Symmetry Space Group P 1 21 1
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 2M 2014-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 2.25 57.6 99.3 0.073 0.997 11.2 5 48308 57.9
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 2.25 2.31 99.1 0.769 0.798 2.9 5.1
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 4KW5 2.25 57.6 45918 2370 99.21 0.18745 0.18579 0.185 0.21913 0.2177 RANDOM 58.465
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] 0.87 -2.66 1.93 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.702 r_dihedral_angle_3_deg 16.214 r_dihedral_angle_4_deg 15.259 r_dihedral_angle_1_deg 6.168 r_long_range_B_refined 5.743 r_mcangle_it 2.392 r_scbond_it 2.024 r_angle_refined_deg 1.628 r_mcbond_it 1.471 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.702 r_dihedral_angle_3_deg 16.214 r_dihedral_angle_4_deg 15.259 r_dihedral_angle_1_deg 6.168 r_long_range_B_refined 5.743 r_mcangle_it 2.392 r_scbond_it 2.024 r_angle_refined_deg 1.628 r_mcbond_it 1.471 r_chiral_restr 0.112 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 6259 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing