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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjugate at 2.03 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 Bis-Tris pH 7, 1.5 M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.89 57.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.769 α = 90 b = 96.769 β = 90 c = 184.207 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 2024-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920194 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 2.03 34.43 98.8 0.314 0.326 0.088 0.781 10 26.1 28337
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 2.03 2.08 97.4 2.838 2.99 0.904 0.988 20
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 2.03 34.43 26934 1396 98.69 0.21142 0.20973 0.2117 0.24365 0.2481 RANDOM 31.758
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] -0.17 -0.17 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.382 r_dihedral_angle_3_deg 13.645 r_long_range_B_refined 8.352 r_long_range_B_other 8.317 r_dihedral_angle_1_deg 6.48 r_scangle_other 6.242 r_scbond_other 4.44 r_scbond_it 4.437 r_mcangle_it 4.372 r_mcangle_other 4.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.382 r_dihedral_angle_3_deg 13.645 r_long_range_B_refined 8.352 r_long_range_B_other 8.317 r_dihedral_angle_1_deg 6.48 r_scangle_other 6.242 r_scbond_other 4.44 r_scbond_it 4.437 r_mcangle_it 4.372 r_mcangle_other 4.371 r_mcbond_it 2.99 r_mcbond_other 2.985 r_angle_refined_deg 1.774 r_angle_other_deg 0.719 r_chiral_restr 0.119 r_gen_planes_other 0.012 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d r_dihedral_angle_4_deg 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 2375 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing