3ORK

Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MRUPDB ENTRY 1MRU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1827727% PEG 3350, 100mM Tris pH 8.5, 200mM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3547.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.341α = 90
b = 51.603β = 90
c = 155.126γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2004-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.65097.90.03418.23.841724
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)
1.61.6988.20.3153.43.1

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 1MRU1.6203954521541000.142910.140860.18037RANDOM14.178
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]
0.61-0.16-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.57
r_dihedral_angle_4_deg17.058
r_dihedral_angle_3_deg11.473
r_dihedral_angle_1_deg5.716
r_scangle_it4.312
r_scbond_it2.866
r_mcangle_it1.894
r_angle_refined_deg1.488
r_rigid_bond_restr1.205
r_mcbond_it1.172
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.57
r_dihedral_angle_4_deg17.058
r_dihedral_angle_3_deg11.473
r_dihedral_angle_1_deg5.716
r_scangle_it4.312
r_scbond_it2.866
r_mcangle_it1.894
r_angle_refined_deg1.488
r_rigid_bond_restr1.205
r_mcbond_it1.172
r_angle_other_deg0.893
r_mcbond_other0.351
r_symmetry_vdw_refined0.3
r_symmetry_vdw_other0.292
r_xyhbond_nbd_refined0.235
r_symmetry_hbond_refined0.229
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2094
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms45

Software

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