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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjugate at 1.74 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 25 % v/v Glycerol, 0.05 M Bis-Tris pH 7, 1.4 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.79 55.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.648 α = 90 b = 96.648 β = 90 c = 184.208 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 1.74 34.17 100 0.176 0.182 0.048 1 18.9 27 45057
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 1.74 1.77 2.499 2.593 0.69 0.328
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 1.74 34.17 45056 2314 99.971 0.205 0.2039 0.2038 0.2272 0.227 RANDOM 35.218
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] -0.278 -0.278 0.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.654 r_dihedral_angle_3_deg 12.549 r_lrange_it 10.87 r_dihedral_angle_2_deg 9.132 r_scangle_it 7.689 r_dihedral_angle_1_deg 6.252 r_scbond_it 5.615 r_mcangle_it 4.465 r_mcbond_it 3.208 r_angle_refined_deg 1.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.654 r_dihedral_angle_3_deg 12.549 r_lrange_it 10.87 r_dihedral_angle_2_deg 9.132 r_scangle_it 7.689 r_dihedral_angle_1_deg 6.252 r_scbond_it 5.615 r_mcangle_it 4.465 r_mcbond_it 3.208 r_angle_refined_deg 1.825 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.216 r_nbd_refined 0.199 r_chiral_restr 0.131 r_xyhbond_nbd_refined 0.117 r_symmetry_xyhbond_nbd_refined 0.115 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms 82 Solvent Atoms 159 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing