3MBQ

Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Brucella melitensis, orthorhombic crystal form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290HR CRYSTAL HT SCREEN, E5: 2M AMMONIUM SUPHATE, 5% ISO-PROPANOL, BRABA.10050.A AT 9.7MG/ML, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.1442.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.56α = 90
b = 95.89β = 90
c = 100.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2010-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.1501000.10919.548.92927729269-325.79
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.151000.5244.792101

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 1dup modified with ccp4 program chainsaw2.147.942927729092147699.60.1690.1690.1660.208RANDOM7.58
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]
-0.120.22-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.706
r_dihedral_angle_4_deg16.425
r_dihedral_angle_3_deg10.82
r_dihedral_angle_1_deg6.34
r_scangle_it4.327
r_scbond_it2.64
r_mcangle_it1.525
r_angle_refined_deg1.464
r_angle_other_deg0.866
r_mcbond_it0.823
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.706
r_dihedral_angle_4_deg16.425
r_dihedral_angle_3_deg10.82
r_dihedral_angle_1_deg6.34
r_scangle_it4.327
r_scbond_it2.64
r_mcangle_it1.525
r_angle_refined_deg1.464
r_angle_other_deg0.866
r_mcbond_it0.823
r_mcbond_other0.218
r_chiral_restr0.093
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3068
Nucleic Acid Atoms
Solvent Atoms345
Heterogen Atoms70

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling