4CKX

Structure of the Mycobacterium tuberculosis Type II Dehydroquinase N12S mutant (Crystal Form 2)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.526% PEG 8000, 0.2 M NA-K PHOSPHATE, 0.1 M TRIS-HCL PH 8.5
Crystal Properties
Matthew coefficientSolvent content
2.957.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.61α = 90
b = 125.61β = 90
c = 125.61γ = 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)2013-10-08MSINGLE 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
12.672.521000.0916.16.95170-330.4
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)
12.62.741000.456.8

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 2Y712.622.21491423899.750.145060.142560.19809RANDOM34.462
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_deg30.651
r_dihedral_angle_3_deg14.494
r_dihedral_angle_4_deg13.636
r_dihedral_angle_1_deg6.465
r_scbond_it5.144
r_mcangle_it4.228
r_mcbond_it2.672
r_scangle_it2.19
r_angle_refined_deg1.474
r_angle_other_deg0.771
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.651
r_dihedral_angle_3_deg14.494
r_dihedral_angle_4_deg13.636
r_dihedral_angle_1_deg6.465
r_scbond_it5.144
r_mcangle_it4.228
r_mcbond_it2.672
r_scangle_it2.19
r_angle_refined_deg1.474
r_angle_other_deg0.771
r_mcbond_other0.615
r_nbd_refined0.239
r_symmetry_vdw_refined0.206
r_xyhbond_nbd_refined0.186
r_nbtor_refined0.179
r_nbd_other0.177
r_symmetry_vdw_other0.162
r_symmetry_hbond_refined0.13
r_nbtor_other0.084
r_chiral_restr0.079
r_xyhbond_nbd_other0.023
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_scbond_other
r_metal_ion_other
r_metal_ion_refined
r_mcangle_other
r_symmetry_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_hbond_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 Atoms1018
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing