2XB8

Structure of Mycobacterium tuberculosis type II dehydroquinase in complex with inhibitor compound (2R)-2-(4-methoxybenzyl)-3- dehydroquinic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.520 MG/ML DEHYDROQUINASE, 0.05 M TRIS-HCL PH 7.5, 1 MM EDTA, 0.2 M SODIUM CHLORIDE, 12.5 MM (2R)-2-PARA-METHOXYBENZYL-3-DEHYDROQUINIC ACID, 5% (V/V) METHANOL, 32% (V/V) 2-METHYL-2,4-PENTANEDIOL, 0.3 M AMMONIUM SULPHATE, 0.1 M HEPES-NAOH PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.52α = 90
b = 126.52β = 90
c = 126.52γ = 90
Symmetry
Space GroupF 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY2010-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.4381000.12610.9670728.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.531000.38211

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1H0S2.42061755031000.16020.156390.20594RANDOM16.109
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.954
r_dihedral_angle_4_deg15.53
r_dihedral_angle_3_deg14.235
r_dihedral_angle_1_deg7.322
r_scangle_it3.015
r_scbond_it1.955
r_angle_refined_deg1.554
r_mcangle_it1.461
r_angle_other_deg0.979
r_mcbond_it0.803
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.954
r_dihedral_angle_4_deg15.53
r_dihedral_angle_3_deg14.235
r_dihedral_angle_1_deg7.322
r_scangle_it3.015
r_scbond_it1.955
r_angle_refined_deg1.554
r_mcangle_it1.461
r_angle_other_deg0.979
r_mcbond_it0.803
r_symmetry_vdw_other0.255
r_symmetry_vdw_refined0.229
r_symmetry_hbond_refined0.216
r_nbd_refined0.215
r_nbd_other0.187
r_xyhbond_nbd_refined0.175
r_nbtor_refined0.165
r_mcbond_other0.133
r_chiral_restr0.096
r_nbtor_other0.085
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1071
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing