4AOZ

B. subtilis dUTPase YncF in complex with dU, PPi and Mg (P212121)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XCDPDB ENTRY 2XCD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
150.2M NACL, 0.1M NA ACETATE PH 5, 20% PEG 6K
Crystal Properties
Matthews coefficientSolvent content
2.3547.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.27α = 90
b = 71.534β = 90
c = 92.299γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2012-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
12.0550.1399.40.116.77.3296821
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)
12.052.1696.90.34.44.4

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 2XCD2.0556.5428124150199.240.161690.158980.21288RANDOM12.119
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]
-0.980.490.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.719
r_dihedral_angle_4_deg17.836
r_dihedral_angle_3_deg14.16
r_dihedral_angle_1_deg6.562
r_scangle_it3.675
r_scbond_it2.282
r_angle_refined_deg1.612
r_mcangle_it1.347
r_angle_other_deg0.861
r_mcbond_it0.741
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.719
r_dihedral_angle_4_deg17.836
r_dihedral_angle_3_deg14.16
r_dihedral_angle_1_deg6.562
r_scangle_it3.675
r_scbond_it2.282
r_angle_refined_deg1.612
r_mcangle_it1.347
r_angle_other_deg0.861
r_mcbond_it0.741
r_mcbond_other0.177
r_chiral_restr0.09
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_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 Atoms3304
Nucleic Acid Atoms
Solvent Atoms566
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing