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Mycobacterium tuberculosis DprE1 mutant Y314C in complex with TCA1
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 291 0.2 M imidazole pH 7.5, 30 - 35% (vol/vol) polypropyleneglycol 400
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.61 α = 90 b = 83.77 β = 103.18 c = 80.62 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 2013-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.2 83.7 99.2 0.05 0.999 13.1 3.7 50740 50.3
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 2.2 2.26 98.9 0.579 0.811 2.4 3.8
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 4KW5 2.2 83.7 48146 2574 99.1 0.19782 0.19639 0.1958 0.22384 0.2235 RANDOM 46.12
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] -0.13 -3.64 2.53 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.09 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_4_deg 15.716 r_dihedral_angle_1_deg 6.37 r_long_range_B_refined 5.805 r_mcangle_it 2.714 r_scbond_it 1.981 r_mcbond_it 1.612 r_angle_refined_deg 1.568 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.09 r_dihedral_angle_3_deg 15.862 r_dihedral_angle_4_deg 15.716 r_dihedral_angle_1_deg 6.37 r_long_range_B_refined 5.805 r_mcangle_it 2.714 r_scbond_it 1.981 r_mcbond_it 1.612 r_angle_refined_deg 1.568 r_chiral_restr 0.105 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 6529 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing