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The Structure and Mechanism of NOV1, a Resveratrol-Cleaving Dioxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.16 M MgCl2, 0.08 M Tris pH 8.5, 18% (w/v) PEG 4000, and 20% glycerol
Crystal Properties Matthews coefficient Solvent content 3.11 60.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.246 α = 90 b = 101.122 β = 90 c = 144.581 γ = 90
Symmetry Space Group I 2 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 NOIR-1 2014-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 50 93.6 0.1 22.3 6.3 68233 19.5427222283
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 53.2 0.51 1.44 2.8
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 5J53 1.75 49.58 1.33 63823 1998 93.21 0.1409 0.1401 0.1436 0.1665 0.1702 27.46
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 14.7870251031 f_angle_d 0.974820763407 f_chiral_restr 0.0595820916535 f_bond_d 0.0099893479103 f_plane_restr 0.00732450001347
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3815 Nucleic Acid Atoms Solvent Atoms 542 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling