5XLW

Mycobacterium tuberculosis Pantothenate kinase mutant F247A/F254A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GEU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.52952% PEG 400, 2.0 M Ammonium sulphate, 100mM HEPES sodium salt
Crystal Properties
Matthews coefficientSolvent content
3.6866.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.33α = 90
b = 119.33β = 90
c = 127.44γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.95372ESRFBM14

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
12.2643.5599.70.08215.57.549403
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)
12.262.381000.4983.77.2

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 REPLACEMENTTHROUGHOUT2GEU2.2643.5546901250099.520.192850.190980.22796RANDOM41.687
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]
-0.7-0.35-0.72.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.445
r_dihedral_angle_3_deg19.252
r_dihedral_angle_4_deg18.123
r_long_range_B_refined9.693
r_long_range_B_other9.692
r_scangle_other7.312
r_dihedral_angle_1_deg6.634
r_mcangle_it5.815
r_mcangle_other5.815
r_scbond_it4.858
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.445
r_dihedral_angle_3_deg19.252
r_dihedral_angle_4_deg18.123
r_long_range_B_refined9.693
r_long_range_B_other9.692
r_scangle_other7.312
r_dihedral_angle_1_deg6.634
r_mcangle_it5.815
r_mcangle_other5.815
r_scbond_it4.858
r_scbond_other4.856
r_mcbond_it3.962
r_mcbond_other3.957
r_angle_refined_deg2.045
r_angle_other_deg1.007
r_chiral_restr0.132
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.006
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4652
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms123

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing