3EHW

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q5UPDB ENTRY 1Q5U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M HEPES buffer, containing 20% PEG 3350 and 200 mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8934.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.446α = 90
b = 87.16β = 90.09
c = 70.608γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmBENT, VERTICALLY FOCUSING MIRROR2004-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8031EMBL/DESY, HAMBURGX13

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
11.82095.80.07110.152.177041770417-326.26
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)
11.81.997.40.4752.242.1310689

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1Q5U1.8206684266842357495.840.159720.15760.19898RANDOM23.11
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]
-0.84-0.070.240.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.116
r_dihedral_angle_4_deg17.146
r_dihedral_angle_3_deg13.382
r_dihedral_angle_1_deg6.439
r_scangle_it5.14
r_scbond_it3.446
r_mcangle_it1.52
r_angle_refined_deg1.289
r_mcbond_it0.875
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.116
r_dihedral_angle_4_deg17.146
r_dihedral_angle_3_deg13.382
r_dihedral_angle_1_deg6.439
r_scangle_it5.14
r_scbond_it3.446
r_mcangle_it1.52
r_angle_refined_deg1.289
r_mcbond_it0.875
r_nbtor_refined0.314
r_nbd_refined0.195
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.174
r_xyhbond_nbd_refined0.156
r_chiral_restr0.079
r_metal_ion_refined0.016
r_bond_refined_d0.01
r_gen_planes_refined0.005
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_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 Atoms6346
Nucleic Acid Atoms
Solvent Atoms731
Heterogen Atoms176

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling