4U63

Crystal structure of a bacterial class III photolyase from Agrobacterium tumefaciens at 1.67A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U3C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.82823 M ammonium sulfate, 10% (v/v) glycerol, 75 mM sodium chloride, 12.5 mM tris (hydroxymethyl) amino methane, 1.25 mM ethylenediaminetetraacetic acid.
Crystal Properties
Matthews coefficientSolvent content
3.5164.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.867α = 90
b = 81.867β = 90
c = 195.952γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2010-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918420BESSY14.1

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
11.6734.31000.08513.79.2891588915821.5
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)
11.671.761000.932.39

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 REPLACEMENTTHROUGHOUT1U3C1.6734.384703433099.920.157360.15620.18047RANDOM30.121
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]
0.870.430.87-2.82
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.229
r_bond_refined_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3799
Nucleic Acid Atoms
Solvent Atoms547
Heterogen Atoms164

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing