4OW8

Crystal structure of kinase domain of PknA from Mtb


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.25 M NaCl, 1.1 M (NH4)2SO4, 0.1 M Bis-Tris (pH 6.5)
Crystal Properties
Matthews coefficientSolvent content
2.0740.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.139α = 90
b = 58.412β = 96.2
c = 78.867γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateVarimax Optics2013-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.0346.8499.80.05722.961591615916-319.1
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)
12.032.1498.80.23810.35.4

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 REPLACEMENTTHROUGHOUT1O6Y2.0346.841512479199.820.228460.226010.2749RANDOM23.41
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]
-0.160.990.15-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.027
r_dihedral_angle_4_deg20.31
r_dihedral_angle_3_deg16.706
r_dihedral_angle_1_deg6.225
r_long_range_B_refined3.64
r_long_range_B_other3.636
r_mcangle_it2.146
r_mcangle_other2.145
r_scangle_other2.033
r_angle_refined_deg1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.027
r_dihedral_angle_4_deg20.31
r_dihedral_angle_3_deg16.706
r_dihedral_angle_1_deg6.225
r_long_range_B_refined3.64
r_long_range_B_other3.636
r_mcangle_it2.146
r_mcangle_other2.145
r_scangle_other2.033
r_angle_refined_deg1.38
r_mcbond_it1.328
r_mcbond_other1.328
r_scbond_it1.258
r_scbond_other1.251
r_angle_other_deg0.792
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
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 Atoms2037
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms11

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
SCALAdata scaling
PHASERphasing