5LFA

Crystal structure of iron-sulfur cluster containing bacterial (6-4) photolyase PhrB - Y424F mutant with impaired DNA repair activity


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DJA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298100 MM MES, 5% PEG400, PH 6.0,
Crystal Properties
Matthews coefficientSolvent content
2.4850.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.183α = 90
b = 94.441β = 90
c = 103.579γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2014-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.96863ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.569.7999.510.20.9635.35.31965721
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)
12.52.561000.752.15.3

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 REPLACEMENTTHROUGHOUT4DJA2.569.7918586103199.510.183880.180710.23961RANDOM30.516
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]
0.370.34-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.756
r_dihedral_angle_2_deg29.245
r_dihedral_angle_4_deg15.551
r_sphericity_bonded13.222
r_dihedral_angle_3_deg13.122
r_dihedral_angle_1_deg5.039
r_long_range_B_other3.539
r_long_range_B_refined3.538
r_mcangle_it2.711
r_mcangle_other2.711
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.756
r_dihedral_angle_2_deg29.245
r_dihedral_angle_4_deg15.551
r_sphericity_bonded13.222
r_dihedral_angle_3_deg13.122
r_dihedral_angle_1_deg5.039
r_long_range_B_other3.539
r_long_range_B_refined3.538
r_mcangle_it2.711
r_mcangle_other2.711
r_scangle_other2.532
r_rigid_bond_restr2.346
r_mcbond_it1.935
r_mcbond_other1.928
r_scbond_it1.92
r_scbond_other1.919
r_angle_refined_deg1.303
r_angle_other_deg0.97
r_chiral_restr0.069
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3916
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
PHASERphasing