4DJA

Crystal structure of a prokaryotic (6-4) photolyase PhrB from Agrobacterium Tumefaciens with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore at 1.45A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherUNPUBLISHED STRUCTURAL DATA OF FE-EDGE SAD-PHASING (WAVELENGTH:1.741) - 2ND CRYSTAL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298100 mM MES, 4% PEG400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.4850.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.388α = 90
b = 106.786β = 90
c = 55.913γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2011-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
11.4572.3695.60.037224.410496410496415.9
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)
11.451.53780.3772.73.111597

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD/MOLECULAR REPLACEMENTTHROUGHOUTUNPUBLISHED STRUCTURAL DATA OF FE-EDGE SAD-PHASING (WAVELENGTH:1.741) - 2ND CRYSTAL1.4519.959970992395487492.670.139950.139950.137790.18049RANDOM19.13
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]
0.01-0.040.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.183
r_dihedral_angle_4_deg17.228
r_dihedral_angle_3_deg12.293
r_dihedral_angle_1_deg5.198
r_angle_refined_deg1.517
r_chiral_restr0.126
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4089
Nucleic Acid Atoms
Solvent Atoms836
Heterogen Atoms97

Software

Software
Software NamePurpose
MAR345data collection
SHELXCDphasing
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling