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Structure of the Mycobacterium tuberculosis Type II Dehydroquinase inhibited by a 3-dehydroquinic acid derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y71 PDB ENTRY 2Y71
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 32% (V/V) 2-METHYL-2,4-PENTANEDIOL, 0.3 M AMMONIUM SULFATE, 0.1 M 4-(2-HYDROXYETHYL)-PIPERAZINE- 1-ETHANESULFONIC ACID SODIUM SALT (HEPES) PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.8 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.003 α = 90 b = 126.003 β = 90 c = 126.003 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 PIXEL DECTRIS PILATUS 6M CYLINDRICAL GRAZING INCIDENCE MIRROR 2013-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 3.1 44.55 100 0.11 19.9 9.8 3177 -3 39
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 3.1 3.27 100 0.35 7.6 9.7
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 2Y71 3.1 44.59 2970 137 99.9 0.13607 0.13199 0.14 0.22814 0.2296 RANDOM 47.75
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 34.295 r_dihedral_angle_4_deg 13.305 r_dihedral_angle_3_deg 12.865 r_dihedral_angle_1_deg 6.56 r_scbond_it 6.425 r_mcangle_it 4.858 r_mcbond_it 2.938 r_scangle_it 2.44 r_angle_refined_deg 1.393 r_angle_other_deg 0.785
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.295 r_dihedral_angle_4_deg 13.305 r_dihedral_angle_3_deg 12.865 r_dihedral_angle_1_deg 6.56 r_scbond_it 6.425 r_mcangle_it 4.858 r_mcbond_it 2.938 r_scangle_it 2.44 r_angle_refined_deg 1.393 r_angle_other_deg 0.785 r_mcbond_other 0.553 r_symmetry_hbond_refined 0.257 r_xyhbond_nbd_refined 0.226 r_nbd_refined 0.214 r_symmetry_vdw_other 0.189 r_nbd_other 0.175 r_nbtor_refined 0.172 r_symmetry_vdw_refined 0.096 r_nbtor_other 0.085 r_chiral_restr 0.067 r_xyhbond_nbd_other 0.035 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1051 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALE data scaling MOLREP phasing