4APZ

Structure of B. subtilis genomic dUTPase YncF in complex with dU, PPi and Mg in P1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.630% MPD, 0.1 M SODIUM ACETATE PH 4.6, 0.02 M CACL2
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.06α = 89.72
b = 97.07β = 88.47
c = 193.85γ = 90.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2011-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I24DiamondI24

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
12.0136.4496.70.095.92.24347551
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)
12.012.0695.90.42.42.2

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 2XCD2.0136.444347552296796.740.171220.169090.21185RANDOM22.493
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]
-0.36-0.30.01-0.650.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.691
r_dihedral_angle_4_deg16.815
r_dihedral_angle_3_deg14.992
r_dihedral_angle_1_deg6.438
r_angle_refined_deg1.902
r_angle_other_deg1.31
r_chiral_restr0.113
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.691
r_dihedral_angle_4_deg16.815
r_dihedral_angle_3_deg14.992
r_dihedral_angle_1_deg6.438
r_angle_refined_deg1.902
r_angle_other_deg1.31
r_chiral_restr0.113
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.004
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms54570
Nucleic Acid Atoms
Solvent Atoms4726
Heterogen Atoms1258

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing