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Stilbene dioxygenase (NOV1) from Novosphingobium aromaticivorans: Ser283Phe mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 sitting drop vapour diffusion, 0.16 M MgCl2, 0.08 M Tris/HCl pH 8.5, 18% wt/vol PEG 4000, and 20% vol/vol glycerol
Crystal Properties Matthews coefficient Solvent content 2.66 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.471 α = 90 b = 187.984 β = 90 c = 105.867 γ = 90
Symmetry Space Group C 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 PIXEL DECTRIS EIGER X 16M 2020-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999977 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.9 50 91.9 0.121 0.092 0.146 0.079 0.981 6.1 3.5 36348
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) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.03 97.5 0.917 0.731 1.121 0.627 0.302 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 5J55 2.9 49.04 34650 1698 91.18 0.2178 0.2141 0.2176 0.291 0.2861 RANDOM 67.13
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] 6.1 -3.77 -2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.778 r_dihedral_angle_4_deg 18.749 r_dihedral_angle_3_deg 18.446 r_dihedral_angle_1_deg 8.046 r_angle_refined_deg 1.436 r_angle_other_deg 1.196 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.778 r_dihedral_angle_4_deg 18.749 r_dihedral_angle_3_deg 18.446 r_dihedral_angle_1_deg 8.046 r_angle_refined_deg 1.436 r_angle_other_deg 1.196 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11322 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 9
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing