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Re-refinement of the 2XRY X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XRY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.5 M LITHIUM SULFATE, 7.5% (W/V) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.69 54.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.77 α = 90 b = 69.77 β = 90 c = 243.08 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315r 2008-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.88567 ESRF ID29
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2XRY 1.5 19.94 1.38 87280 1305 89.85 0.1704 0.17 0.1858 0.1987 0.2101
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.238 f_angle_d 1.488 f_chiral_restr 0.072 f_bond_d 0.018 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3677 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 110
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing