1RN8

Crystal structure of dUTPase complexed with substrate analogue imido-dUTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EUWPDB ENTRY 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
2.5451.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.618α = 90
b = 74.618β = 90
c = 99.58γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8110EMBL/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
11.9327.199.20.06110.31012768
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)
1.931.9899.20.2682.87.56819

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 1EUW1.9320121441214462499.20.1640.139060.137010.18017RANDOM17.402
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]
0.110.050.11-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it9.889
r_scbond_it7.274
r_dihedral_angle_1_deg6.006
r_mcangle_it4.827
r_mcbond_it2.733
r_angle_refined_deg1.603
r_angle_other_deg0.869
r_symmetry_vdw_other0.355
r_nbd_other0.259
r_symmetry_hbond_refined0.232
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it9.889
r_scbond_it7.274
r_dihedral_angle_1_deg6.006
r_mcangle_it4.827
r_mcbond_it2.733
r_angle_refined_deg1.603
r_angle_other_deg0.869
r_symmetry_vdw_other0.355
r_nbd_other0.259
r_symmetry_hbond_refined0.232
r_xyhbond_nbd_refined0.23
r_symmetry_vdw_refined0.204
r_nbd_refined0.191
r_chiral_restr0.09
r_nbtor_other0.085
r_bond_refined_d0.016
r_bond_other_d0.008
r_gen_planes_refined0.005
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1089
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing