4B0H

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AOZPDB ENTRY 4AOZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
150.2 M LICL, 0.1 M NA ACETATE PH 5.0, 20 % (W/V) PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.3246.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.03α = 90
b = 71.31β = 90
c = 91.88γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.1835.0192.80.158.17.3132942
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)
11.181.241001.332.27.3

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 4AOZ1.1835.04132942705892.790.119240.117120.16006RANDOM15.003
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]
0.19-0.08-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free75.558
r_dihedral_angle_2_deg34.851
r_dihedral_angle_4_deg19.361
r_sphericity_bonded15.958
r_dihedral_angle_3_deg13.232
r_dihedral_angle_1_deg7.304
r_rigid_bond_restr5.625
r_angle_refined_deg2.302
r_angle_other_deg1.013
r_chiral_restr0.147
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free75.558
r_dihedral_angle_2_deg34.851
r_dihedral_angle_4_deg19.361
r_sphericity_bonded15.958
r_dihedral_angle_3_deg13.232
r_dihedral_angle_1_deg7.304
r_rigid_bond_restr5.625
r_angle_refined_deg2.302
r_angle_other_deg1.013
r_chiral_restr0.147
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3329
Nucleic Acid Atoms
Solvent Atoms924
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing