1OKB

crystal structure of Uracil-DNA glycosylase from Atlantic cod (Gadus morhua)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1M HEPES PH 7.5, 1.4M SODIUM CITRATE
Crystal Properties
Matthews coefficientSolvent content
2.7154.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.58α = 90
b = 67.189β = 119.86
c = 68.644γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMAR scanner 345 mm plate2001-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM1AESRFBM1A

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
11.91298.70.09610.23.34216219.45
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)
11.9297.50.52222.9

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 1AKZ1.91242162211298.70.18610.18610.2057RANDOM22.4043
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]
1.6232.017-3.1291.506
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.207
c_scangle_it3.184
c_scbond_it2.125
c_mcangle_it2.003
c_mcbond_it1.291
c_angle_deg1.189
c_improper_angle_d0.832
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.207
c_scangle_it3.184
c_scbond_it2.125
c_mcangle_it2.003
c_mcbond_it1.291
c_angle_deg1.189
c_improper_angle_d0.832
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3574
Nucleic Acid Atoms
Solvent Atoms343
Heterogen Atoms14

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALAdata scaling
CNSphasing