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Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with inhibitor 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbath on oil 7.5 298 potassium bromate
Peg 2000mme, pH 7.5, microbath on oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.59 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.84 α = 90 b = 137.52 β = 95.88 c = 148.33 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315r mirrors 2009-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97910 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 2.5 62.3 87 0.127 5.2 2.6 133469 115676 2 2
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 2.5 2.6 84 0.552 1.3 2.5 16264
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3N7A 2.5 62.3 2 115676 109823 5817 86.65 0.229 0.20588 0.20114 0.1998 0.29528 0.2914 RANDOM 33.898
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] 0.03 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.371 r_dihedral_angle_3_deg 19.265 r_dihedral_angle_4_deg 17.151 r_dihedral_angle_1_deg 6.968 r_scangle_it 2.878 r_scbond_it 1.709 r_angle_refined_deg 1.623 r_mcangle_it 1.24 r_mcbond_it 0.672 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.371 r_dihedral_angle_3_deg 19.265 r_dihedral_angle_4_deg 17.151 r_dihedral_angle_1_deg 6.968 r_scangle_it 2.878 r_scbond_it 1.709 r_angle_refined_deg 1.623 r_mcangle_it 1.24 r_mcbond_it 0.672 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24999 Nucleic Acid Atoms Solvent Atoms 1555 Heterogen Atoms 266
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling