1SEH

Crystal structure of E. coli dUTPase complexed with the product dUMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EUW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8293PEG 3350, SODIUM ACETATE, TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.257α = 90
b = 75.257β = 90
c = 100.532γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8040EMBL/DESY, HAMBURGX11

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
11.472099.90.08327.631.829251-3
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)
11.471.61000.734.8620.096421

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 REPLACEMENTTHROUGHOUT1EUW1.47202776727767148499.980.158950.158950.157650.18384RANDOM22.137
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]
-0.08-0.04-0.080.11
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it10.238
r_scbond_it6.951
r_dihedral_angle_1_deg5.589
r_mcangle_it3.739
r_mcbond_it1.891
r_angle_refined_deg1.379
r_angle_other_deg0.737
r_symmetry_vdw_other0.295
r_nbd_other0.248
r_symmetry_hbond_refined0.214
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it10.238
r_scbond_it6.951
r_dihedral_angle_1_deg5.589
r_mcangle_it3.739
r_mcbond_it1.891
r_angle_refined_deg1.379
r_angle_other_deg0.737
r_symmetry_vdw_other0.295
r_nbd_other0.248
r_symmetry_hbond_refined0.214
r_nbd_refined0.182
r_symmetry_vdw_refined0.154
r_xyhbond_nbd_refined0.152
r_nbtor_other0.083
r_chiral_restr0.076
r_bond_refined_d0.021
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1056
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
MOLREPphasing