3KGB

Crystal structure of thymidylate synthase 1/2 from Encephalitozoon cuniculi at 2.2 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2TSRPDB entry 2TSR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5290MOLECULAR DIMENSIONS PACT SCREEN CONDITION A10: 200mM MgCl2, 100mM Na-ACETATE pH 5.0, 20% PEG 6000. ECNUA.01191.A AT 11mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.4148.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.63α = 90
b = 72.28β = 90
c = 61.68γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442009-10-23MSINGLE 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 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
12.22098.60.08819.566.91681816581-335.25
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)
12.22.2698.40.5714.16.51216

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2TSR2.220165811658183898.60.2070.2070.2050.246RANDOM13.46
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]
-1.69-0.071.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.906
r_dihedral_angle_4_deg21.782
r_dihedral_angle_3_deg14.693
r_dihedral_angle_1_deg6.226
r_scangle_it3.557
r_scbond_it2.3
r_angle_refined_deg1.475
r_mcangle_it1.398
r_angle_other_deg0.941
r_mcbond_it0.737
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.906
r_dihedral_angle_4_deg21.782
r_dihedral_angle_3_deg14.693
r_dihedral_angle_1_deg6.226
r_scangle_it3.557
r_scbond_it2.3
r_angle_refined_deg1.475
r_mcangle_it1.398
r_angle_other_deg0.941
r_mcbond_it0.737
r_mcbond_other0.166
r_chiral_restr0.097
r_bond_refined_d0.016
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1968
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms1

Software

Software
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling