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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
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 3 58.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.95 α = 90 b = 126.95 β = 90 c = 126.95 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 PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR) 2013-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
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 1.65 38.28 99.9 0.08 13 5.4 20465 -3 13
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 1.65 1.74 100 0.33 4.8 5.4
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 2Y71 1.65 38.31 19394 1045 99.91 0.10466 0.10258 0.123 0.14434 0.1596 RANDOM 17.468
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 33.206 r_sphericity_free 30.46 r_mcangle_it 15.585 r_scbond_it 15.316 r_sphericity_bonded 12.127 r_mcbond_it 11.923 r_dihedral_angle_3_deg 11.356 r_dihedral_angle_4_deg 10.977 r_scangle_it 7.977 r_dihedral_angle_1_deg 5.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.206 r_sphericity_free 30.46 r_mcangle_it 15.585 r_scbond_it 15.316 r_sphericity_bonded 12.127 r_mcbond_it 11.923 r_dihedral_angle_3_deg 11.356 r_dihedral_angle_4_deg 10.977 r_scangle_it 7.977 r_dihedral_angle_1_deg 5.422 r_mcbond_other 4.447 r_rigid_bond_restr 3.213 r_angle_refined_deg 1.537 r_angle_other_deg 0.894 r_symmetry_vdw_refined 0.329 r_nbd_refined 0.305 r_symmetry_vdw_other 0.236 r_nbd_other 0.177 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.112 r_metal_ion_refined 0.086 r_nbtor_other 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1016 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALE data scaling MOLREP phasing