2WQ6

Structure of the 6-4 photolyase of D. melanogaster in complex with the non-natural N4-methyl T(Dewar)C lesion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CVUPDB ENTRY 3CVU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1291100 MM HEPES, PH 7, 13-17% PEG1500, 18C
Crystal Properties
Matthews coefficientSolvent content
2.9558

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.169α = 90
b = 87.486β = 90
c = 91.856γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DASLSX06DA

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
12.343.7399.30.0618.1432351242.4
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)
12.32.4299.70.43.94.1

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 3CVU2.343.7430688162099.170.202650.201290.22848RANDOM27.233
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]
0.020.88-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.493
r_dihedral_angle_4_deg15.619
r_dihedral_angle_3_deg13.928
r_dihedral_angle_1_deg4.998
r_scangle_it4.127
r_scbond_it2.685
r_mcangle_it1.959
r_angle_refined_deg1.22
r_mcbond_it1.041
r_angle_other_deg0.933
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.493
r_dihedral_angle_4_deg15.619
r_dihedral_angle_3_deg13.928
r_dihedral_angle_1_deg4.998
r_scangle_it4.127
r_scbond_it2.685
r_mcangle_it1.959
r_angle_refined_deg1.22
r_mcbond_it1.041
r_angle_other_deg0.933
r_mcbond_other0.221
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.005
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_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 Atoms4162
Nucleic Acid Atoms609
Solvent Atoms170
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing