2HQU

Human dUTPase in complex with alpha,beta-iminodUTP and magnesium ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q5UPDB entry 1Q5U truncated at residue 146

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529318-20% PEG 3350, 0.1M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.6826.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.409α = 90
b = 71.773β = 90
c = 76.475γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrorMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8124EMBL/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
12.12099.10.1169.211.22142021420-328.8
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)
12.12.2990.333.691.22736

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 1Q5U truncated at residue 1462.220177391773994599.110.202230.202230.199680.25065RANDOM20.252
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]
-2.1-0.923.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.176
r_dihedral_angle_4_deg22.048
r_dihedral_angle_3_deg17.468
r_dihedral_angle_1_deg6.536
r_scangle_it2.256
r_scbond_it1.571
r_angle_refined_deg1.415
r_mcangle_it0.863
r_mcbond_it0.497
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.176
r_dihedral_angle_4_deg22.048
r_dihedral_angle_3_deg17.468
r_dihedral_angle_1_deg6.536
r_scangle_it2.256
r_scbond_it1.571
r_angle_refined_deg1.415
r_mcangle_it0.863
r_mcbond_it0.497
r_nbtor_refined0.315
r_symmetry_vdw_refined0.283
r_nbd_refined0.21
r_xyhbond_nbd_refined0.187
r_symmetry_hbond_refined0.179
r_metal_ion_refined0.118
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3022
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing