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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-AGCT DNA conjugate at 2.47 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 291.15 0.05 M Lithium sulfate, 0.05 M HEPES pH 6.5, 1.4 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.25 62.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.48 α = 90 b = 123.48 β = 90 c = 127.088 γ = 90
Symmetry Space Group P 4 21 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 2023-06-15 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 2.47 37.33 100 0.861 0.893 0.234 0.991 5 27.2 35897
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) 2.47 2.57 100 7.643 7.923 2.082 0.665 1.1 27.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.47 37.326 35730 1848 99.543 0.217 0.2155 0.2151 0.2395 0.2403 RANDOM 48.394
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] -1.768 -1.768 3.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.334 r_dihedral_angle_3_deg 11.017 r_lrange_it 10.734 r_scangle_it 9.072 r_dihedral_angle_2_deg 6.645 r_mcangle_it 6.421 r_scbond_it 6.186 r_dihedral_angle_1_deg 6.012 r_mcbond_it 4.503 r_angle_refined_deg 0.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.334 r_dihedral_angle_3_deg 11.017 r_lrange_it 10.734 r_scangle_it 9.072 r_dihedral_angle_2_deg 6.645 r_mcangle_it 6.421 r_scbond_it 6.186 r_dihedral_angle_1_deg 6.012 r_mcbond_it 4.503 r_angle_refined_deg 0.859 r_nbtor_refined 0.302 r_symmetry_nbd_refined 0.208 r_nbd_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.115 r_xyhbond_nbd_refined 0.107 r_ncsr_local_group_1 0.065 r_chiral_restr 0.04 r_bond_refined_d 0.004 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4667 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement Coot model building DIALS data reduction Aimless data scaling PHASER phasing