3LD9

Crystal structure of thymidylate kinase from Ehrlichia chaffeensis at 2.15A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PBRPDB ENTRY 2PBR MODIFIED WITH CCP4 PROGRAM CHAINSAW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5290MD PACT SCREEN G8: 100MM BIS-TRIS-PROPANE PH 7.5, 200MM NA-SULPHATE, 20% PEG 3350; EHCHA.01616.A AT 25.5MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.0439.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.17α = 90
b = 144.82β = 90
c = 146.84γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rSingle crystal, cylindrically bent, Si(220)2009-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9744ALS5.0.1

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
12.15501000.07916.845.94672746708-3
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)
12.152.2199.90.4813.75.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 2PBR MODIFIED WITH CCP4 PROGRAM CHAINSAW2.1546.374672744279235499.970.188830.186560.2322RANDOM31.523
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]
0.47-2.031.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.035
r_dihedral_angle_4_deg22.633
r_dihedral_angle_3_deg13.267
r_dihedral_angle_1_deg5.192
r_scangle_it3.36
r_scbond_it2.112
r_angle_refined_deg1.345
r_mcangle_it1.295
r_angle_other_deg0.906
r_mcbond_it0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.035
r_dihedral_angle_4_deg22.633
r_dihedral_angle_3_deg13.267
r_dihedral_angle_1_deg5.192
r_scangle_it3.36
r_scbond_it2.112
r_angle_refined_deg1.345
r_mcangle_it1.295
r_angle_other_deg0.906
r_mcbond_it0.71
r_mcbond_other0.208
r_chiral_restr0.076
r_bond_refined_d0.014
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5700
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms28

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling