2HRM

Crystal structure of dUTPase complexed with substrate analogue methylene-dUTP


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
2.5752.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.65α = 90
b = 75.65β = 90
c = 101.558γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrorMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.8500EMBL/DESY, HAMBURGBW7B

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
11.72099.10.04814.53.161927619276-328.27
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)
11.71.899.40.4572.43.193034

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 REPLACEMENTTHROUGHOUT1EUW1.720182831828398799.130.169560.169560.168230.19559RANDOM21.045
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]
-0.01-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.746
r_dihedral_angle_4_deg20.198
r_dihedral_angle_3_deg12.259
r_scangle_it6.903
r_dihedral_angle_1_deg5.482
r_scbond_it5.33
r_mcangle_it2.926
r_mcbond_it1.702
r_angle_refined_deg1.677
r_angle_other_deg0.861
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.746
r_dihedral_angle_4_deg20.198
r_dihedral_angle_3_deg12.259
r_scangle_it6.903
r_dihedral_angle_1_deg5.482
r_scbond_it5.33
r_mcangle_it2.926
r_mcbond_it1.702
r_angle_refined_deg1.677
r_angle_other_deg0.861
r_symmetry_vdw_other0.213
r_nbd_refined0.19
r_nbd_other0.182
r_xyhbond_nbd_refined0.173
r_symmetry_hbond_refined0.17
r_nbtor_refined0.158
r_symmetry_vdw_refined0.135
r_mcbond_other0.116
r_chiral_restr0.112
r_nbtor_other0.081
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1012
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing