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Crystal structure of Mycobacterium tuberculosis Type II Dehydroquinase D88N mutant 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 6.2 28% PEG4000, 100 MM NA-CITRATE PH 6.2
Crystal Properties Matthews coefficient Solvent content 1.99 38.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.848 α = 90 b = 65.187 β = 90 c = 94.755 γ = 90
Symmetry Space Group P 2 21 21
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) 2014-02-01 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 1.55 94.75 95.6 0.08 15 5.5 34076 -3 14.9
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 1.55 1.63 76.2 0.36 2.9 2.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Y71 1.55 53.71 32331 1701 95.24 0.13799 0.13524 0.18931 0.2148 RANDOM 19.382
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] 0.38 -0.02 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.361 r_sphericity_free 27.883 r_mcangle_it 14.872 r_scbond_it 14.398 r_dihedral_angle_4_deg 12.913 r_dihedral_angle_3_deg 11.947 r_sphericity_bonded 11.769 r_mcbond_it 11.758 r_scangle_it 7.962 r_dihedral_angle_1_deg 5.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.361 r_sphericity_free 27.883 r_mcangle_it 14.872 r_scbond_it 14.398 r_dihedral_angle_4_deg 12.913 r_dihedral_angle_3_deg 11.947 r_sphericity_bonded 11.769 r_mcbond_it 11.758 r_scangle_it 7.962 r_dihedral_angle_1_deg 5.449 r_mcbond_other 4.339 r_rigid_bond_restr 2.566 r_angle_refined_deg 1.465 r_angle_other_deg 0.811 r_symmetry_vdw_refined 0.255 r_nbd_refined 0.252 r_nbtor_refined 0.175 r_nbd_other 0.169 r_symmetry_vdw_other 0.164 r_xyhbond_nbd_refined 0.116 r_symmetry_hbond_refined 0.095 r_nbtor_other 0.09 r_chiral_restr 0.089 r_symmetry_metal_ion_refined 0.083 r_metal_ion_refined 0.08 r_bond_refined_d 0.012 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_other r_symmetry_hbond_other 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 2129 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing