3ORP

Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 5)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
172771M Sodium citrate, 100mM Tris pH 7.0, 200mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3748.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.185α = 90
b = 52.164β = 90
c = 155.652γ = 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 8.3.1ALS8.3.1

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
12.12090.30.04224.23.216500
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)
2.12.1760.30.1633.22.5

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 1MRU2.119.991650088190.30.1910.1880.238RANDOM40.904
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]
3.87-0.72-3.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.416
r_dihedral_angle_4_deg18.58
r_dihedral_angle_3_deg13.858
r_dihedral_angle_1_deg6.964
r_scangle_it2.91
r_scbond_it1.884
r_angle_refined_deg1.607
r_mcangle_it1.188
r_mcbond_it1.058
r_angle_other_deg0.851
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.416
r_dihedral_angle_4_deg18.58
r_dihedral_angle_3_deg13.858
r_dihedral_angle_1_deg6.964
r_scangle_it2.91
r_scbond_it1.884
r_angle_refined_deg1.607
r_mcangle_it1.188
r_mcbond_it1.058
r_angle_other_deg0.851
r_symmetry_hbond_refined0.307
r_symmetry_vdw_other0.276
r_nbd_refined0.209
r_symmetry_vdw_refined0.201
r_nbd_other0.188
r_nbtor_refined0.173
r_mcbond_other0.166
r_xyhbond_nbd_refined0.162
r_chiral_restr0.089
r_nbtor_other0.086
r_bond_refined_d0.014
r_gen_planes_refined0.005
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 Atoms2101
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms31

Software

Software
Software NamePurpose
Blu-Icedata collection
EPMRphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling