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Structure of Mycobacterium tuberculosis Type II Dehydroquinase inhibited by (2R)-2-(benzothiophen-5-yl)methyl-3-dehydroquinic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H0S PDB ENTRY 1H0S
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 SODIUM SALT), PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.267 α = 90 b = 126.267 β = 90 c = 126.267 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 CCD ADSC QUANTUM 315r KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS 2010-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 38 99.9 0.06 7.5 6.6 24676 18.8
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 99.7 0.38 2.1 5.8
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 1H0S 1.54 38.07 23379 1296 99.85 0.1362 0.13454 0.143 0.16556 0.1774 RANDOM 14.547
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 32.926 r_dihedral_angle_3_deg 12.469 r_dihedral_angle_4_deg 8.985 r_scangle_it 5.627 r_dihedral_angle_1_deg 5.44 r_scbond_it 3.772 r_mcangle_it 2.493 r_mcbond_it 1.588 r_angle_refined_deg 1.564 r_rigid_bond_restr 1.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.926 r_dihedral_angle_3_deg 12.469 r_dihedral_angle_4_deg 8.985 r_scangle_it 5.627 r_dihedral_angle_1_deg 5.44 r_scbond_it 3.772 r_mcangle_it 2.493 r_mcbond_it 1.588 r_angle_refined_deg 1.564 r_rigid_bond_restr 1.522 r_angle_other_deg 1.017 r_symmetry_hbond_other 0.48 r_mcbond_other 0.457 r_symmetry_hbond_refined 0.281 r_nbd_refined 0.235 r_symmetry_vdw_other 0.235 r_symmetry_vdw_refined 0.223 r_xyhbond_nbd_refined 0.204 r_nbd_other 0.182 r_nbtor_refined 0.176 r_chiral_restr 0.108 r_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1023 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing