3EHI

Crystal Structure of Human Thymidyalte Synthase M190K with Loop 181-197 stabilized in the inactive conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YPV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52912.0M AS, 0.1M Tris pH 8.5, 20mM BME, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.261.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.053α = 90
b = 96.053β = 90
c = 80.064γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.003APS22-BM

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
125088.40.04759.70711.729397260211
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)
122.0740.80.4592.41177

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 DIFFRACTIONTHROUGHOUT2YPV241.592939725970132188.40.20.1980.238RANDOM56.7
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]
0.130.060.13-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.851
r_dihedral_angle_4_deg20.269
r_dihedral_angle_3_deg18.097
r_dihedral_angle_1_deg7.498
r_scangle_it4.568
r_scbond_it3.086
r_mcangle_it2.035
r_angle_refined_deg1.915
r_mcbond_it1.252
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.851
r_dihedral_angle_4_deg20.269
r_dihedral_angle_3_deg18.097
r_dihedral_angle_1_deg7.498
r_scangle_it4.568
r_scbond_it3.086
r_mcangle_it2.035
r_angle_refined_deg1.915
r_mcbond_it1.252
r_nbtor_refined0.315
r_nbd_refined0.229
r_symmetry_vdw_refined0.221
r_xyhbond_nbd_refined0.184
r_symmetry_hbond_refined0.182
r_chiral_restr0.152
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2220
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms14

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
CNSphasing