2XRZ

X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei in complex with intact CPD-lesion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSTRUCTURAL DATA OF NATIVE M. MAZEI PHOTOLYASE.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.60.2 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6, 10% (W/V) PEG 4000, 10% (V/V) GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.7359.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.7α = 90
b = 116.2β = 90
c = 168.3γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.229.4899.90.0817.54.972130-335.6
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)
12.22.321000.692.64.9

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 REPLACEMENTTHROUGHOUTSTRUCTURAL DATA OF NATIVE M. MAZEI PHOTOLYASE.2.229.4870962109499.940.170930.170360.20819SHELLS47.114
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]
0.4-1.360.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.28
r_dihedral_angle_4_deg15.683
r_dihedral_angle_3_deg13.769
r_dihedral_angle_1_deg5.37
r_scangle_it2.177
r_scbond_it1.389
r_angle_refined_deg1.363
r_angle_other_deg0.952
r_mcangle_it0.887
r_mcbond_it0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.28
r_dihedral_angle_4_deg15.683
r_dihedral_angle_3_deg13.769
r_dihedral_angle_1_deg5.37
r_scangle_it2.177
r_scbond_it1.389
r_angle_refined_deg1.363
r_angle_other_deg0.952
r_mcangle_it0.887
r_mcbond_it0.46
r_mcbond_other0.113
r_chiral_restr0.071
r_bond_refined_d0.012
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_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 Atoms7125
Nucleic Acid Atoms1017
Solvent Atoms635
Heterogen Atoms153

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing