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Crystal structure of M.tuberculosis imidazole glycerol phosphate dehydratase in complex with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GQU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 293.15 20% PEG1500, 0.2M sodium citrate tribasic dehydrate, 0.1M Tris HCL, pH 9.0
Crystal Properties Matthews coefficient Solvent content 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.829 α = 90 b = 111.829 β = 90 c = 111.829 γ = 90
Symmetry Space Group P 4 3 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 IMAGE PLATE RIGAKU RAXIS IV++ 2020-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 2.2 35 100 0.92 13.56 21.5 12742
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 2.2 2.28 0.718
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4GQU 2.2 33.74 12742 628 99.922 0.158 0.1557 0.1646 0.2048 0.2074 24.539
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.17 r_dihedral_angle_4_deg 15.53 r_dihedral_angle_3_deg 15.454 r_dihedral_angle_1_deg 7.491 r_lrange_it 5.181 r_lrange_other 5.153 r_scangle_it 3.831 r_scangle_other 3.829 r_mcangle_it 2.642 r_mcangle_other 2.641
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.17 r_dihedral_angle_4_deg 15.53 r_dihedral_angle_3_deg 15.454 r_dihedral_angle_1_deg 7.491 r_lrange_it 5.181 r_lrange_other 5.153 r_scangle_it 3.831 r_scangle_other 3.829 r_mcangle_it 2.642 r_mcangle_other 2.641 r_scbond_it 2.416 r_scbond_other 2.415 r_mcbond_it 1.716 r_mcbond_other 1.708 r_angle_refined_deg 1.577 r_angle_other_deg 1.358 r_symmetry_xyhbond_nbd_refined 0.222 r_nbd_other 0.214 r_nbd_refined 0.197 r_symmetry_nbd_other 0.189 r_symmetry_nbd_refined 0.163 r_xyhbond_nbd_refined 0.161 r_nbtor_refined 0.154 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1457 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing