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Crystal Structure of the Bacteriophage T4 recombination mediator protein UvsY, Lattice Type III
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZWR PDB entry 4ZWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 1:1 UvsY (10 mg/mL, 150 mM sodium chloride, 20 mM HEPES, pH 7.5, 2 mM DTT) to 10% Jeffamine T-403, 10% Jeffamine ED-2003, 100 mM Tris-HCl, pH 8.0 in the presence of 750 uM dA3 oligonucleotide
Crystal Properties Matthews coefficient Solvent content 3.3 62.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.571 α = 90 b = 123.571 β = 90 c = 332.465 γ = 120
Symmetry Space Group P 65 2 2
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 2015-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.6 45.262 99.9 0.104 0.118 11.26 4.55 87352 -3 67.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.76 99.7 1.795 2.035 0.91 3.9
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 PDB entry 4ZWR 2.6 45.262 1.34 87310 3698 99.92 0.2037 0.2023 0.2114 0.2363 0.2413 71.1781
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 11.722 f_angle_d 0.973 f_chiral_restr 0.043 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5732 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling Coot model building PHASER phasing