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Crystal structure of iron-sulfur cluster containing photolyase PhrB mutant I51W
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DJA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 5% PEG 400
0.1 M MES at pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.54 51.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.607 α = 90 b = 107.243 β = 90 c = 113.672 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 CCD MARMOSAIC 300 mm CCD 2015-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.149 44.655 99.2 11.1 7 65431
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 4DJA 2.149 44.655 1.34 64829 3307 98.84 0.1663 0.1637 0.1655 0.2129 0.2152
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 15.214 f_angle_d 0.969 f_chiral_restr 0.055 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8233 Nucleic Acid Atoms Solvent Atoms 619 Heterogen Atoms 146
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction