3ORO

Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 4)


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 Sodium Citrate, 100mM CHES pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1141.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.598α = 90
b = 51.423β = 90
c = 135.327γ = 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 8.3.11.107ALS8.3.1

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
11.92098.60.05513.53.321540
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)
11.9294.80.2135.22.8

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 1mru1.917.4621540116198.40.194740.192960.22758RANDOM27.779
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]
-0.120.18-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.988
r_dihedral_angle_3_deg13.28
r_dihedral_angle_4_deg12.875
r_dihedral_angle_1_deg5.046
r_scangle_it2.056
r_angle_refined_deg1.518
r_scbond_it1.415
r_mcangle_it0.804
r_angle_other_deg0.744
r_mcbond_it0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.988
r_dihedral_angle_3_deg13.28
r_dihedral_angle_4_deg12.875
r_dihedral_angle_1_deg5.046
r_scangle_it2.056
r_angle_refined_deg1.518
r_scbond_it1.415
r_mcangle_it0.804
r_angle_other_deg0.744
r_mcbond_it0.71
r_nbd_refined0.203
r_symmetry_vdw_other0.191
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.171
r_symmetry_hbond_refined0.168
r_nbd_other0.167
r_symmetry_vdw_refined0.128
r_chiral_restr0.123
r_mcbond_other0.101
r_nbtor_other0.08
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
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 Atoms2048
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms44

Software

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