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Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with compound 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Hepes, pH7.5
peg 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.66 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.41 α = 90 b = 126.41 β = 90 c = 126.41 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 IMAGE PLATE MAR scanner 345 mm plate Si(111) monochromator. Mirror 1: Grazing angle 2.8 mrad, vertical focusing. Mir
ror 2: vertical and horizontal focusing. 2009-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97825 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 31.6 99.8 0.133 0.121 5.5 4.8 13318 13302 2 2 17.725
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 98.5 0.805 0.53 1 4.6 1929
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1H0R 1.9 31.6 2 13318 12624 654 99.92 0.18572 0.17753 0.17528 0.22147 0.1697 RANDOM 19.439
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 31.078 r_dihedral_angle_3_deg 15.295 r_dihedral_angle_4_deg 12.644 r_dihedral_angle_1_deg 7.505 r_scangle_it 4.928 r_scbond_it 3.216 r_angle_refined_deg 2.104 r_mcangle_it 2.068 r_mcbond_it 1.308 r_chiral_restr 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.078 r_dihedral_angle_3_deg 15.295 r_dihedral_angle_4_deg 12.644 r_dihedral_angle_1_deg 7.505 r_scangle_it 4.928 r_scbond_it 3.216 r_angle_refined_deg 2.104 r_mcangle_it 2.068 r_mcbond_it 1.308 r_chiral_restr 0.169 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 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 1083 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 22
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling