☰ Navigation Tabs
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 20% PEG1500, 0.2M sodium citrate tribasic dehydrate, 0.1M Tris HCL, pH 9.0
Crystal Properties Matthews coefficient Solvent content 2.64 53.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.116 α = 90 b = 113.116 β = 90 c = 113.116 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++ 2021-03-04 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 1.848 35 100 0.96 34.5 36.8 21801
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 1.848 1.92 0.79
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4gqu 1.848 34.129 21801 1088 99.927 0.156 0.1546 0.1678 0.1836 0.1947 5 23.873
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 35.957 r_dihedral_angle_3_deg 13.954 r_dihedral_angle_4_deg 12.912 r_dihedral_angle_1_deg 7.454 r_lrange_it 5.798 r_lrange_other 5.641 r_scangle_it 4.468 r_scangle_other 4.466 r_scbond_it 3.079 r_scbond_other 3.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.957 r_dihedral_angle_3_deg 13.954 r_dihedral_angle_4_deg 12.912 r_dihedral_angle_1_deg 7.454 r_lrange_it 5.798 r_lrange_other 5.641 r_scangle_it 4.468 r_scangle_other 4.466 r_scbond_it 3.079 r_scbond_other 3.077 r_mcangle_it 2.614 r_mcangle_other 2.613 r_angle_other_deg 2.502 r_angle_refined_deg 1.829 r_mcbond_it 1.825 r_mcbond_other 1.795 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.233 r_nbd_other 0.233 r_symmetry_nbd_other 0.231 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.11 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.035 r_gen_planes_other 0.013 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_symmetry_xyhbond_nbd_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1456 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing