☰ 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, HANGING DROP 9 293 20% PEG 1500, 0.2M sodium citrate tribasic dehydrate, 0.1M Tris HCL, pH 9.0
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.1 α = 90 b = 112.1 β = 90 c = 112.1 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++ 2020-12-01 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 2.28 35 99.9 0.94 21.58 29.3 11541
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 2.28 2.36 0.66
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 2.28 28.041 11541 587 99.818 0.162 0.1591 0.1682 0.2099 0.2135 28.777
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 35.285 r_dihedral_angle_3_deg 16.027 r_dihedral_angle_4_deg 13.944 r_dihedral_angle_1_deg 7.34 r_lrange_it 5.774 r_lrange_other 5.731 r_scangle_it 4.379 r_scangle_other 4.377 r_mcangle_it 3.091 r_mcangle_other 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.285 r_dihedral_angle_3_deg 16.027 r_dihedral_angle_4_deg 13.944 r_dihedral_angle_1_deg 7.34 r_lrange_it 5.774 r_lrange_other 5.731 r_scangle_it 4.379 r_scangle_other 4.377 r_mcangle_it 3.091 r_mcangle_other 3.09 r_scbond_it 2.826 r_scbond_other 2.824 r_mcbond_it 2.026 r_mcbond_other 2.022 r_angle_refined_deg 1.538 r_angle_other_deg 1.325 r_nbd_other 0.223 r_symmetry_nbd_refined 0.197 r_symmetry_nbd_other 0.195 r_nbd_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.153 r_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_other 0.091 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1459 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing