1W2Y

The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue dUpNHp


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OGKPDB ENTRY 1OGK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1725-30% MPD, 5% ISOPROPANOL, 50 MM MG-ACETATE, 100 MM HEPES PH 7.0
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.963α = 90
b = 70.629β = 90
c = 92.85γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002003-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.655099.40.06345.2530612.7
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)
11.651.7198.50.452.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1OGK1.6555.9501852693990.1530.1510.194RANDOM29.23
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]
0.4-0.23-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.643
r_dihedral_angle_4_deg25.195
r_dihedral_angle_3_deg13.27
r_scangle_it5.414
r_dihedral_angle_1_deg4.872
r_scbond_it4.327
r_mcangle_it2.599
r_mcbond_it2.134
r_angle_refined_deg1.581
r_angle_other_deg1.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.643
r_dihedral_angle_4_deg25.195
r_dihedral_angle_3_deg13.27
r_scangle_it5.414
r_dihedral_angle_1_deg4.872
r_scbond_it4.327
r_mcangle_it2.599
r_mcbond_it2.134
r_angle_refined_deg1.581
r_angle_other_deg1.222
r_symmetry_vdw_other0.254
r_nbd_refined0.248
r_symmetry_vdw_refined0.232
r_symmetry_hbond_refined0.222
r_xyhbond_nbd_refined0.195
r_nbtor_refined0.194
r_nbd_other0.178
r_chiral_restr0.104
r_nbtor_other0.089
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3599
Nucleic Acid Atoms
Solvent Atoms383
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing