4V0S

Crystal structure of Mycobacterium tuberculosis Type II Dehydroquinase D88N mutant inhibited by a 3-dehydroquinic acid derivative


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.228% PEG4000, 100 MM NA-CITRATE PH 6.2
Crystal Properties
Matthews coefficientSolvent content
1.9938.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.848α = 90
b = 65.187β = 90
c = 94.755γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MPLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR)2014-02-01MSINGLE 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
11.5594.7595.60.08155.534076-314.9
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)
11.551.6376.20.362.92.6

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 2Y711.5553.7132331170195.240.137990.135240.18931RANDOM19.382
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]
0.38-0.02-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.361
r_sphericity_free27.883
r_mcangle_it14.872
r_scbond_it14.398
r_dihedral_angle_4_deg12.913
r_dihedral_angle_3_deg11.947
r_sphericity_bonded11.769
r_mcbond_it11.758
r_scangle_it7.962
r_dihedral_angle_1_deg5.449
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.361
r_sphericity_free27.883
r_mcangle_it14.872
r_scbond_it14.398
r_dihedral_angle_4_deg12.913
r_dihedral_angle_3_deg11.947
r_sphericity_bonded11.769
r_mcbond_it11.758
r_scangle_it7.962
r_dihedral_angle_1_deg5.449
r_mcbond_other4.339
r_rigid_bond_restr2.566
r_angle_refined_deg1.465
r_angle_other_deg0.811
r_symmetry_vdw_refined0.255
r_nbd_refined0.252
r_nbtor_refined0.175
r_nbd_other0.169
r_symmetry_vdw_other0.164
r_xyhbond_nbd_refined0.116
r_symmetry_hbond_refined0.095
r_nbtor_other0.09
r_chiral_restr0.089
r_symmetry_metal_ion_refined0.083
r_metal_ion_refined0.08
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2129
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms101

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing