☰ Navigation Tabs
Structure of Mycobacterium tuberculosis type II dehydroquinase in complex with inhibitor compound (2R)-2-(4-methoxybenzyl)-3- dehydroquinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H0S PDB ENTRY 1H0S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 20 MG/ML DEHYDROQUINASE, 0.05 M TRIS-HCL PH 7.5, 1 MM EDTA, 0.2 M SODIUM CHLORIDE, 12.5 MM (2R)-2-PARA-METHOXYBENZYL-3-DEHYDROQUINIC ACID, 5% (V/V) METHANOL, 32% (V/V) 2-METHYL-2,4-PENTANEDIOL, 0.3 M AMMONIUM SULPHATE, 0.1 M HEPES-NAOH PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.52 α = 90 b = 126.52 β = 90 c = 126.52 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY 2010-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 38 100 0.12 6 10.9 6707 28.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.38 2 11
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 PDB ENTRY 1H0S 2.4 20 6175 503 100 0.1602 0.15639 0.159 0.20594 0.2025 RANDOM 16.109
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 32.954 r_dihedral_angle_4_deg 15.53 r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 7.322 r_scangle_it 3.015 r_scbond_it 1.955 r_angle_refined_deg 1.554 r_mcangle_it 1.461 r_angle_other_deg 0.979 r_mcbond_it 0.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.954 r_dihedral_angle_4_deg 15.53 r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 7.322 r_scangle_it 3.015 r_scbond_it 1.955 r_angle_refined_deg 1.554 r_mcangle_it 1.461 r_angle_other_deg 0.979 r_mcbond_it 0.803 r_symmetry_vdw_other 0.255 r_symmetry_vdw_refined 0.229 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.215 r_nbd_other 0.187 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.165 r_mcbond_other 0.133 r_chiral_restr 0.096 r_nbtor_other 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined 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 1071 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing