3ORL

Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 3)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.527725% PEG 3350, 100mM Tris pH 8.5, 200mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0138.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.191α = 90
b = 50.633β = 90
c = 132.762γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.8927ALS8.3.1

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
12.92099.70.08711.13.76052
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)
2.93.0699.90.4063.13.6

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 1mru2.92060523381000.213790.210570.27658RANDOM41.378
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]
1.78-2.590.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.413
r_dihedral_angle_4_deg14.475
r_dihedral_angle_3_deg13.981
r_dihedral_angle_1_deg3.736
r_angle_refined_deg1
r_nbtor_refined0.296
r_nbd_refined0.207
r_symmetry_vdw_refined0.176
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.413
r_dihedral_angle_4_deg14.475
r_dihedral_angle_3_deg13.981
r_dihedral_angle_1_deg3.736
r_angle_refined_deg1
r_nbtor_refined0.296
r_nbd_refined0.207
r_symmetry_vdw_refined0.176
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.141
r_chiral_restr0.059
r_bond_refined_d0.011
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1981
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms32

Software

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