2HR6

Crystal structure of dUTPase in complex with substrate analogue dUDP and manganese


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829320% PEG 3350, 0.2M SODIUM ACETATE, 0.1M TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4950.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.049α = 90
b = 75.049β = 90
c = 99.936γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirror2002-03-17MSINGLE 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
11.8424.9980.06410.812.61470314703-322.35
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)
11.841.89980.5581.310.1815

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 REPLACEMENTTHROUGHOUT1EUW1.8424.9139531395374998.10.151680.151680.150540.17338RANDOM22.763
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]
-0.09-0.04-0.090.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.32
r_dihedral_angle_4_deg16.193
r_dihedral_angle_3_deg12.121
r_scangle_it7.993
r_scbond_it6.01
r_dihedral_angle_1_deg5.818
r_mcangle_it3.606
r_mcbond_it2.23
r_angle_refined_deg1.702
r_angle_other_deg0.821
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.32
r_dihedral_angle_4_deg16.193
r_dihedral_angle_3_deg12.121
r_scangle_it7.993
r_scbond_it6.01
r_dihedral_angle_1_deg5.818
r_mcangle_it3.606
r_mcbond_it2.23
r_angle_refined_deg1.702
r_angle_other_deg0.821
r_symmetry_hbond_refined0.284
r_symmetry_vdw_other0.251
r_nbd_refined0.215
r_xyhbond_nbd_refined0.203
r_nbd_other0.191
r_symmetry_vdw_refined0.171
r_nbtor_refined0.164
r_chiral_restr0.098
r_mcbond_other0.093
r_nbtor_other0.082
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1013
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing