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Glutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-GC DNA conjugate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R6S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20 % v/v Glycerol, 5 % w/v PEG 3350, 0.05 M Bis-Tris pH 7, 1 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.44 64.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.525 α = 90 b = 122.525 β = 90 c = 136.661 γ = 90
Symmetry Space Group I 4 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 EIGER2 XE 16M 2023-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976284 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.73 53.65 100 0.381 0.395 0.105 0.995 7.4 26.7 14176
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.73 2.86 100 2.667 2.764 0.726 0.865 1.7 27.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.73 50.911 14147 674 99.767 0.188 0.1865 0.1864 0.2197 0.2197 58.77
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] 3.04 3.04 -6.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.006 r_dihedral_angle_3_deg 15.443 r_dihedral_angle_6_deg 14.506 r_lrange_it 12.189 r_scangle_it 9.918 r_mcangle_it 8.888 r_scbond_it 7.134 r_dihedral_angle_1_deg 6.615 r_mcbond_it 6.032 r_angle_refined_deg 1.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.006 r_dihedral_angle_3_deg 15.443 r_dihedral_angle_6_deg 14.506 r_lrange_it 12.189 r_scangle_it 9.918 r_mcangle_it 8.888 r_scbond_it 7.134 r_dihedral_angle_1_deg 6.615 r_mcbond_it 6.032 r_angle_refined_deg 1.861 r_nbtor_refined 0.314 r_symmetry_nbd_refined 0.227 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.118 r_symmetry_xyhbond_nbd_refined 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2357 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement Coot model building DIALS data reduction Aimless data scaling PHASER phasing