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Crystal structure of Mycobacterium tuberculosis type 2 dehydroquinase in complex with(1R,4R,5R)-1,4,5-trihydroxy-3-((1S)-1-hydroxy-2-phenyl) ethylcyclohex-2-en-1-carboxylic acid
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 2.9 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.36 α = 90 b = 126.36 β = 90 c = 126.36 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 2.9 44.67 99.3 0.11 12 4.8 3767 -3 25.6
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 2.9 3.06 100 0.35 4.6 5.1
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 2.9 38.13 3589 168 98.79 0.15348 0.15187 0.1618 0.18867 0.1838 RANDOM 28.072
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 31.17 r_dihedral_angle_4_deg 15.656 r_dihedral_angle_3_deg 14.848 r_dihedral_angle_1_deg 6.675 r_scbond_it 4.693 r_mcangle_it 2.646 r_mcbond_it 1.592 r_scangle_it 1.333 r_angle_refined_deg 1.323 r_angle_other_deg 0.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.17 r_dihedral_angle_4_deg 15.656 r_dihedral_angle_3_deg 14.848 r_dihedral_angle_1_deg 6.675 r_scbond_it 4.693 r_mcangle_it 2.646 r_mcbond_it 1.592 r_scangle_it 1.333 r_angle_refined_deg 1.323 r_angle_other_deg 0.853 r_mcbond_other 0.253 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.192 r_nbd_other 0.173 r_symmetry_vdw_refined 0.172 r_nbtor_refined 0.171 r_symmetry_vdw_other 0.168 r_nbtor_other 0.082 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 1006 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALE data scaling MOLREP phasing