4CIX

Crystal structure of Mycobacterium tuberculosis type 2 dehydroquinase in complex with(1R,4R,5R)-1,4,5-trihydroxy-3-((1S)-1-hydroxy-2-phenyl) ethylcyclohex-2-en-1-carboxylic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.532% (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 coefficientSolvent content
2.958.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.36α = 90
b = 126.36β = 90
c = 126.36γ = 90
Symmetry
Space GroupF 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MCYLINDRICAL GRAZING INCIDENCE MIRROR2013-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.944.6799.30.11124.83767-325.6
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)
12.93.061000.354.65.1

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 REPLACEMENTTHROUGHOUT2Y712.938.13358916898.790.153480.151870.18867RANDOM28.072
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_deg31.17
r_dihedral_angle_4_deg15.656
r_dihedral_angle_3_deg14.848
r_dihedral_angle_1_deg6.675
r_scbond_it4.693
r_mcangle_it2.646
r_mcbond_it1.592
r_scangle_it1.333
r_angle_refined_deg1.323
r_angle_other_deg0.853
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.17
r_dihedral_angle_4_deg15.656
r_dihedral_angle_3_deg14.848
r_dihedral_angle_1_deg6.675
r_scbond_it4.693
r_mcangle_it2.646
r_mcbond_it1.592
r_scangle_it1.333
r_angle_refined_deg1.323
r_angle_other_deg0.853
r_mcbond_other0.253
r_nbd_refined0.221
r_symmetry_hbond_refined0.206
r_xyhbond_nbd_refined0.192
r_nbd_other0.173
r_symmetry_vdw_refined0.172
r_nbtor_refined0.171
r_symmetry_vdw_other0.168
r_nbtor_other0.082
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms1006
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing