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Dioxygenase AsqJ in complex with 2 and alpha-ketoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 100 mM TRIS/HCl, 1 M LiCl, 27% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.09 41.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.31 α = 90 b = 115.9 β = 90 c = 66.72 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 16M 2019-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.1 30 95.1 0.072 9.6 3.8 16153
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 2.1 2.2 96.1 0.643 2.3
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 5DAP 2.1 30 15338 807 95.05 0.1927 0.1915 0.1951 0.216 0.232 RANDOM 50.101
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] -4.72 10.02 -5.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.737 r_dihedral_angle_4_deg 15.677 r_dihedral_angle_3_deg 13.25 r_dihedral_angle_1_deg 6.414 r_angle_refined_deg 1.22 r_angle_other_deg 1.056 r_rigid_bond_restr 0.348 r_chiral_restr 0.038 r_gen_planes_other 0.005 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.737 r_dihedral_angle_4_deg 15.677 r_dihedral_angle_3_deg 13.25 r_dihedral_angle_1_deg 6.414 r_angle_refined_deg 1.22 r_angle_other_deg 1.056 r_rigid_bond_restr 0.348 r_chiral_restr 0.038 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_refined_d 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2218 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing