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2-Ketoglutarate-Dependent Dioxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LNH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 17 mg/mL enzyme was incubated with 9.2 mM L-Ile and grew at 1 M sodium citrate for 15 days
Crystal Properties Matthews coefficient Solvent content 1.89 35.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.145 α = 90 b = 129.628 β = 90 c = 153.684 γ = 90
Symmetry Space Group P 21 21 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 Bruker PHOTON II 2023-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54
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 3.2 23.65 99.8 0.227 7.2 7.7 15586
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 3.2 3.46 0.606
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.2 23.65 14714 826 99.63 0.21863 0.21585 0.2192 0.26674 0.2614 RANDOM 53.796
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] 7.66 -2.55 -5.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.314 r_dihedral_angle_3_deg 17.042 r_dihedral_angle_4_deg 14.121 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 6.204 r_long_range_B_other 6.204 r_mcangle_it 3.893 r_mcangle_other 3.892 r_scangle_other 3.324 r_mcbond_it 2.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.314 r_dihedral_angle_3_deg 17.042 r_dihedral_angle_4_deg 14.121 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 6.204 r_long_range_B_other 6.204 r_mcangle_it 3.893 r_mcangle_other 3.892 r_scangle_other 3.324 r_mcbond_it 2.234 r_mcbond_other 2.234 r_scbond_it 1.867 r_scbond_other 1.866 r_angle_refined_deg 1.158 r_angle_other_deg 0.702 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7536 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing