1OGH

Structure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.53MG/ML PROTEIN VAPOUR DIFFUSION WITH MOTHER LIQUOR: 5% PEG8000, 0.1 M TRIS-HCL, PH8.5, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.4450

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.06α = 90
b = 111.06β = 90
c = 111.06γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I711MAX III711

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
11.88451000.0425211.237385
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)
11.881.9299.90.13621

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSIRASTHROUGHOUT1.8819.653544918611000.1480.1470.184RANDOM15.66
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.816
r_scangle_it4.887
r_scbond_it2.947
r_mcangle_it1.936
r_angle_refined_deg1.637
r_mcbond_it1.02
r_angle_other_deg0.926
r_symmetry_vdw_refined0.363
r_symmetry_vdw_other0.31
r_symmetry_hbond_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.816
r_scangle_it4.887
r_scbond_it2.947
r_mcangle_it1.936
r_angle_refined_deg1.637
r_mcbond_it1.02
r_angle_other_deg0.926
r_symmetry_vdw_refined0.363
r_symmetry_vdw_other0.31
r_symmetry_hbond_refined0.295
r_nbd_other0.243
r_nbd_refined0.193
r_chiral_restr0.176
r_xyhbond_nbd_refined0.173
r_nbtor_other0.086
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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 Atoms2879
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing