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Dioxygenase AsqJ mutant (V72I) 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 293 100 mM HEPES/NaOH, 1.25 M LiBr, 27% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.17 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.41 α = 90 b = 120.43 β = 90 c = 66.87 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 1.55 30 98.5 0.055 14.2 4.5 42718
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 1.55 1.65 98.9 0.564 2.9
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 1.55 30 40575 2135 98.51 0.1478 0.1468 0.1606 0.1687 0.1809 RANDOM 24.965
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] -2.23 2.5 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.411 r_dihedral_angle_4_deg 19.048 r_dihedral_angle_3_deg 12.327 r_dihedral_angle_1_deg 6.722 r_angle_refined_deg 1.224 r_angle_other_deg 1.155 r_rigid_bond_restr 0.319 r_chiral_restr 0.049 r_gen_planes_other 0.007 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.411 r_dihedral_angle_4_deg 19.048 r_dihedral_angle_3_deg 12.327 r_dihedral_angle_1_deg 6.722 r_angle_refined_deg 1.224 r_angle_other_deg 1.155 r_rigid_bond_restr 0.319 r_chiral_restr 0.049 r_gen_planes_other 0.007 r_gen_planes_refined 0.005 r_bond_refined_d 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2219 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing