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Crystal structure of Mycobacterium tuberculosis type 2 dehydroquinase in complex with (1R,4R,5R)-1,4,5-trihydroxy-3-(2-hydroxy)ethylcyclohex-2-ene-1-carboxylic acid
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 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 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.38 α = 90 b = 126.38 β = 90 c = 126.38 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 2.2 38.11 99.2 0.09 11 4.3 8562 -3 17.7
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 2.2 2.32 95.4 0.25 3.8 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Y71 2.2 38.13 8152 409 99.11 0.14416 0.14177 0.1524 0.19227 0.2005 RANDOM 23.361
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 32.459 r_dihedral_angle_4_deg 13.328 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 6.222 r_scbond_it 4.77 r_mcangle_it 3.193 r_mcbond_it 1.955 r_angle_refined_deg 1.517 r_scangle_it 1.514 r_angle_other_deg 0.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.459 r_dihedral_angle_4_deg 13.328 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 6.222 r_scbond_it 4.77 r_mcangle_it 3.193 r_mcbond_it 1.955 r_angle_refined_deg 1.517 r_scangle_it 1.514 r_angle_other_deg 0.896 r_mcbond_other 0.362 r_symmetry_vdw_refined 0.342 r_nbd_refined 0.263 r_symmetry_vdw_other 0.21 r_xyhbond_nbd_refined 0.2 r_nbd_other 0.178 r_symmetry_hbond_refined 0.171 r_nbtor_refined 0.17 r_chiral_restr 0.087 r_nbtor_other 0.083 r_xyhbond_nbd_other 0.07 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 1071 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALE data scaling MOLREP phasing