☰ Navigation Tabs
Crystal structure of Mycobacterium tuberculosis type 2 dehydroquinase in complex with (1R,4R,5R)-1,4,5-trihydroxy-3-((1R)-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 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 2.9 57.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.205 α = 90 b = 126.205 β = 90 c = 126.205 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 2.1 44.62 99.9 0.06 19.8 5.7 9857 -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 2.1 2.21 100 0.39 4.7 5.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Y71 2.1 38.08 9359 472 99.8 0.14802 0.14549 0.19754 0.1947 RANDOM 32.123
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 31.783 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_4_deg 11.903 r_scbond_it 6.743 r_dihedral_angle_1_deg 6.203 r_mcangle_it 4.256 r_mcbond_it 2.792 r_scangle_it 2.122 r_angle_refined_deg 1.558 r_angle_other_deg 0.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.783 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_4_deg 11.903 r_scbond_it 6.743 r_dihedral_angle_1_deg 6.203 r_mcangle_it 4.256 r_mcbond_it 2.792 r_scangle_it 2.122 r_angle_refined_deg 1.558 r_angle_other_deg 0.856 r_mcbond_other 0.661 r_symmetry_vdw_refined 0.361 r_metal_ion_refined 0.357 r_nbd_refined 0.268 r_nbd_other 0.189 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.182 r_symmetry_vdw_other 0.179 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.089 r_nbtor_other 0.087 r_xyhbond_nbd_other 0.046 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.001 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 1032 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing