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Structures of DddQ from Ruegeria lac. Reveal Key Residues for Metal Binding and Catalysis - TRIS bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES pH 6.0, 0.2 M LiCl, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.24 45.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.87 α = 90 b = 87.761 β = 93.37 c = 48.9 γ = 90
Symmetry Space Group P 1 21 1
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 NOIR-1 2015-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.976250 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 48.817 99 0.063 0.088 0.046 14.1 3.7 26468 26468 14.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 99 0.22 0.22 0.31 0.161 3.5 3.6 3853
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4LA2 2 48.816 1.34 26449 1239 98.93 0.1878 0.1854 0.1853 0.2362 0.2331 4.7% 15.904
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 16.759 f_angle_d 0.819 f_chiral_restr 0.05 f_bond_d 0.013 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2941 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction PHASER phasing XDS data scaling