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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjugate at 2.17 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 0.3 M Lithium sulfate, 0.05 M Bis-Tris pH 7, 18 % w/v PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.81 56.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.11 α = 90 b = 97.11 β = 90 c = 183.654 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 2023-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980112 SOLEIL PROXIMA 2
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 2.17 48.56 99.6 0.111 0.116 0.031 0.999 22.4 25.9 23491
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 2.17 2.23 95.2 1.371 1.436 0.42 0.767 2.1 21.5
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 2.17 48.56 22341 1147 99.61 0.2094 0.20796 0.2079 0.2378 0.2377 RANDOM 53.898
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] 0.75 0.75 -1.49
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.517 r_dihedral_angle_3_deg 12.272 r_dihedral_angle_2_deg 8.722 r_dihedral_angle_1_deg 6.863 r_mcangle_it 4.65 r_scbond_it 3.974 r_mcbond_it 3.022 r_angle_refined_deg 1.391 r_chiral_restr 0.072 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.517 r_dihedral_angle_3_deg 12.272 r_dihedral_angle_2_deg 8.722 r_dihedral_angle_1_deg 6.863 r_mcangle_it 4.65 r_scbond_it 3.974 r_mcbond_it 3.022 r_angle_refined_deg 1.391 r_chiral_restr 0.072 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2370 Nucleic Acid Atoms 82 Solvent Atoms 113 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building