4CIY

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


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
2.957.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.205α = 90
b = 126.205β = 90
c = 126.205γ = 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
12.144.6299.90.0619.85.79857-325.6
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)
12.12.211000.394.75.9

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 2Y712.138.08935947299.80.148020.145490.19754RANDOM32.123
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.783
r_dihedral_angle_3_deg14.555
r_dihedral_angle_4_deg11.903
r_scbond_it6.743
r_dihedral_angle_1_deg6.203
r_mcangle_it4.256
r_mcbond_it2.792
r_scangle_it2.122
r_angle_refined_deg1.558
r_angle_other_deg0.856
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.783
r_dihedral_angle_3_deg14.555
r_dihedral_angle_4_deg11.903
r_scbond_it6.743
r_dihedral_angle_1_deg6.203
r_mcangle_it4.256
r_mcbond_it2.792
r_scangle_it2.122
r_angle_refined_deg1.558
r_angle_other_deg0.856
r_mcbond_other0.661
r_symmetry_vdw_refined0.361
r_metal_ion_refined0.357
r_nbd_refined0.268
r_nbd_other0.189
r_xyhbond_nbd_refined0.189
r_nbtor_refined0.182
r_symmetry_vdw_other0.179
r_symmetry_hbond_refined0.131
r_chiral_restr0.089
r_nbtor_other0.087
r_xyhbond_nbd_other0.046
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1032
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing