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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-AGCT DNA conjugate at 1.82 Angstrom resolution
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 0.05 M Lithium sulfate, 0.05 M HEPES pH 6.5, 1.4 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.81 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.794 α = 90 b = 95.794 β = 90 c = 183.006 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 EIGER X 9M 2023-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920105 NSLS-II 17-ID-1
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 1.82 47.9 100 0.089 0.096 0.036 0.998 14 13.5 38517
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) 1.82 1.86 99.8 1.347 1.448 0.529 0.73 1.8 14.1
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 1.82 47.897 38478 1920 99.793 0.219 0.2186 0.2188 0.2348 0.2346 39.465
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] -0.879 -0.879 1.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.937 r_dihedral_angle_6_deg 14.017 r_dihedral_angle_3_deg 12.283 r_lrange_it 8.794 r_scangle_it 7.615 r_dihedral_angle_1_deg 6.446 r_mcangle_it 5.808 r_scbond_it 5.74 r_mcbond_it 4.608 r_angle_refined_deg 1.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.937 r_dihedral_angle_6_deg 14.017 r_dihedral_angle_3_deg 12.283 r_lrange_it 8.794 r_scangle_it 7.615 r_dihedral_angle_1_deg 6.446 r_mcangle_it 5.808 r_scbond_it 5.74 r_mcbond_it 4.608 r_angle_refined_deg 1.435 r_nbtor_refined 0.307 r_nbd_refined 0.191 r_symmetry_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.152 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.082 r_metal_ion_refined 0.051 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2314 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement Coot model building DIALS data reduction Aimless data scaling PHASER phasing