3ORT

Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 6)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MRUPDB entry 1mru

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52771M Na citrate, 100mM CHES pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3948.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.987α = 90
b = 52.099β = 90
c = 143.371γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2003-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.91596.30.04810.43.225114
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.9299.20.3212.73.33733

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 1mru1.915.282373612761000.211220.208610.25972RANDOM48.221
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]
3.66-1.32-2.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.22
r_dihedral_angle_4_deg17.812
r_dihedral_angle_3_deg14.991
r_dihedral_angle_1_deg5.911
r_scangle_it3.049
r_scbond_it1.937
r_angle_refined_deg1.566
r_mcangle_it1.153
r_mcbond_it0.843
r_angle_other_deg0.826
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.22
r_dihedral_angle_4_deg17.812
r_dihedral_angle_3_deg14.991
r_dihedral_angle_1_deg5.911
r_scangle_it3.049
r_scbond_it1.937
r_angle_refined_deg1.566
r_mcangle_it1.153
r_mcbond_it0.843
r_angle_other_deg0.826
r_symmetry_vdw_other0.226
r_nbd_refined0.217
r_nbd_other0.181
r_nbtor_refined0.176
r_mcbond_other0.167
r_xyhbond_nbd_refined0.16
r_symmetry_vdw_refined0.115
r_chiral_restr0.088
r_nbtor_other0.087
r_symmetry_hbond_refined0.045
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2060
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms43

Software

Software
Software NamePurpose
Blu-Icedata collection
EPMRphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling