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X-ray crystallographic structure of (6-4)photolyase from Drosophila melanogaster at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 0.2 M Lithium sulphate, 0.1 M Bis-Tris(pH=6.5), 25%PEG3350, 4% polypropylene glycol p 400
Crystal Properties Matthews coefficient Solvent content 2.6 52.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.903 α = 90 b = 88.933 β = 90 c = 114.022 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.91840 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.79 29.42 99.2 0.99 16.9 12.7 58656 25.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.854 0.83
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 3cvy 1.79 29.42 1.34 58569 1997 99.18 0.1771 0.1761 0.18 0.2062 0.2094 26.96
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 7.9472 f_angle_d 1.205 f_chiral_restr 0.0816 f_bond_d 0.0149 f_plane_restr 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4167 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing