4CIV

Crystal structure of Mycobacterium tuberculosis type 2 dehydroquinase in complex with (1R,4R,5R)-1,4,5-trihydroxy-3-hydroxymethylcyclohex-2-ene-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
2.856.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.18α = 90
b = 126.18β = 90
c = 126.18γ = 90
Symmetry
Space GroupF 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDPT COATED SI MIRROR2012-11-28MSINGLE 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
12.93881.80.0813.35.73103-337.2
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)
12.93.06710.372.22.2

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 2Y712.936.45295814181.550.215370.212410.27937RANDOM37.937
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_deg33.425
r_dihedral_angle_3_deg14.265
r_dihedral_angle_4_deg13.955
r_dihedral_angle_1_deg6.432
r_scbond_it3.676
r_mcangle_it1.901
r_mcbond_it1.073
r_angle_refined_deg1.05
r_scangle_it0.836
r_angle_other_deg0.745
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.425
r_dihedral_angle_3_deg14.265
r_dihedral_angle_4_deg13.955
r_dihedral_angle_1_deg6.432
r_scbond_it3.676
r_mcangle_it1.901
r_mcbond_it1.073
r_angle_refined_deg1.05
r_scangle_it0.836
r_angle_other_deg0.745
r_nbd_refined0.214
r_symmetry_hbond_refined0.199
r_nbd_other0.175
r_symmetry_vdw_other0.174
r_nbtor_refined0.171
r_mcbond_other0.154
r_xyhbond_nbd_refined0.139
r_symmetry_vdw_refined0.129
r_nbtor_other0.079
r_chiral_restr0.054
r_bond_refined_d0.006
r_gen_planes_refined0.003
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 Atoms1038
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing