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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjugate at 2.01 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 0.1 M Sodium chloride, 25 % v/v Glycerol, 0.05 M Bis-Tris pH 7, 1.8 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.063 α = 90 b = 96.063 β = 90 c = 183.858 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 16M 2024-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979098 NSLS-II 17-ID-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 34.34 97.9 0.256 0.266 0.071 0.998 10 26.7 28872
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 2.05 100 4.13 4.279 1.119 0.612 0.9 28
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 2.01 34.34 26734 1425 97.37 0.21234 0.21066 0.2219 0.24216 0.2488 RANDOM 44.726
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] -0.3 -0.3 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.242 r_dihedral_angle_3_deg 13.015 r_dihedral_angle_1_deg 6.898 r_long_range_B_refined 6.498 r_long_range_B_other 6.181 r_scangle_other 4.147 r_mcangle_it 3.179 r_mcangle_other 3.178 r_scbond_it 2.563 r_scbond_other 2.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.242 r_dihedral_angle_3_deg 13.015 r_dihedral_angle_1_deg 6.898 r_long_range_B_refined 6.498 r_long_range_B_other 6.181 r_scangle_other 4.147 r_mcangle_it 3.179 r_mcangle_other 3.178 r_scbond_it 2.563 r_scbond_other 2.491 r_mcbond_it 1.997 r_mcbond_other 1.997 r_angle_refined_deg 1.384 r_angle_other_deg 0.462 r_chiral_restr 0.068 r_gen_planes_other 0.008 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 2357 Nucleic Acid Atoms 62 Solvent Atoms 146 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing