4CIW

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

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.38α = 90
b = 126.38β = 90
c = 126.38γ = 90
Symmetry
Space GroupF 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MPLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR)2013-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOCALBAXALOC

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
12.238.1199.20.09114.38562-317.7
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)
12.22.3295.40.253.82.6

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 2Y712.238.13815240999.110.144160.141770.19227RANDOM23.361
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_deg32.459
r_dihedral_angle_4_deg13.328
r_dihedral_angle_3_deg12.727
r_dihedral_angle_1_deg6.222
r_scbond_it4.77
r_mcangle_it3.193
r_mcbond_it1.955
r_angle_refined_deg1.517
r_scangle_it1.514
r_angle_other_deg0.896
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.459
r_dihedral_angle_4_deg13.328
r_dihedral_angle_3_deg12.727
r_dihedral_angle_1_deg6.222
r_scbond_it4.77
r_mcangle_it3.193
r_mcbond_it1.955
r_angle_refined_deg1.517
r_scangle_it1.514
r_angle_other_deg0.896
r_mcbond_other0.362
r_symmetry_vdw_refined0.342
r_nbd_refined0.263
r_symmetry_vdw_other0.21
r_xyhbond_nbd_refined0.2
r_nbd_other0.178
r_symmetry_hbond_refined0.171
r_nbtor_refined0.17
r_chiral_restr0.087
r_nbtor_other0.083
r_xyhbond_nbd_other0.07
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
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 Atoms81
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing