4CL0

Structure of the Mycobacterium tuberculosis Type II Dehydroquinase inhibited by a 3-dehydroquinic acid derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y71PDB ENTRY 2Y71

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
2.855.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.003α = 90
b = 126.003β = 90
c = 126.003γ = 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
13.144.551000.1119.99.83177-339
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)
13.13.271000.357.69.7

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 2Y713.144.59297013799.90.136070.131990.22814RANDOM47.75
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_deg34.295
r_dihedral_angle_4_deg13.305
r_dihedral_angle_3_deg12.865
r_dihedral_angle_1_deg6.56
r_scbond_it6.425
r_mcangle_it4.858
r_mcbond_it2.938
r_scangle_it2.44
r_angle_refined_deg1.393
r_angle_other_deg0.785
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.295
r_dihedral_angle_4_deg13.305
r_dihedral_angle_3_deg12.865
r_dihedral_angle_1_deg6.56
r_scbond_it6.425
r_mcangle_it4.858
r_mcbond_it2.938
r_scangle_it2.44
r_angle_refined_deg1.393
r_angle_other_deg0.785
r_mcbond_other0.553
r_symmetry_hbond_refined0.257
r_xyhbond_nbd_refined0.226
r_nbd_refined0.214
r_symmetry_vdw_other0.189
r_nbd_other0.175
r_nbtor_refined0.172
r_symmetry_vdw_refined0.096
r_nbtor_other0.085
r_chiral_restr0.067
r_xyhbond_nbd_other0.035
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
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 Atoms1051
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing