2Y71

Structure of Mycobacterium tuberculosis type II dehydroquinase complexed with (1R,4S,5R)-1,4,5-trihydroxy-3-((5-methylbenzo(b) thiophen-2-yl)methoxy)cyclohex-2-enecarboxylate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H0SPDB ENTRY 1H0S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.532% (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 = 126.65α = 90
b = 126.65β = 90
c = 126.65γ = 90
Symmetry
Space GroupF 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rBENT CYLINDRICAL MIRRORS2010-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.529.199.50.067.77.82686617
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)
11.51.5899.80.3724

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 1H0S1.521.412542314431000.126770.124890.161RANDOM13.6
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_deg30.451
r_dihedral_angle_3_deg12.332
r_dihedral_angle_4_deg11.55
r_dihedral_angle_1_deg5.338
r_scangle_it5.217
r_scbond_it3.51
r_mcangle_it2.462
r_mcbond_it1.547
r_angle_refined_deg1.51
r_rigid_bond_restr1.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.451
r_dihedral_angle_3_deg12.332
r_dihedral_angle_4_deg11.55
r_dihedral_angle_1_deg5.338
r_scangle_it5.217
r_scbond_it3.51
r_mcangle_it2.462
r_mcbond_it1.547
r_angle_refined_deg1.51
r_rigid_bond_restr1.304
r_angle_other_deg0.949
r_mcbond_other0.414
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1040
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing