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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjugate at 1.78 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 0.15 M Potassium chloride, 25 % v/v Glycerol, 0.05 M Bis-Tris pH 7, 1.6 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.79 55.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.524 α = 90 b = 96.524 β = 90 c = 184.354 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 1.78 34.13 100 0.189 0.196 0.052 0.999 15.9 27.1 42058
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 1.78 1.82 100 2.749 2.854 0.768 0.334 26.5
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 (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 1.78 34.126 42051 2099 99.948 0.203 0.2017 0.2018 0.2248 0.2249 RANDOM 35.808
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] -0.444 -0.444 0.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.997 r_dihedral_angle_3_deg 12.765 r_dihedral_angle_2_deg 11.065 r_lrange_it 9.495 r_scangle_it 7.763 r_dihedral_angle_1_deg 6.2 r_scbond_it 5.313 r_mcangle_it 4.586 r_mcbond_it 3.235 r_angle_refined_deg 1.845
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.997 r_dihedral_angle_3_deg 12.765 r_dihedral_angle_2_deg 11.065 r_lrange_it 9.495 r_scangle_it 7.763 r_dihedral_angle_1_deg 6.2 r_scbond_it 5.313 r_mcangle_it 4.586 r_mcbond_it 3.235 r_angle_refined_deg 1.845 r_nbtor_refined 0.314 r_symmetry_nbd_refined 0.214 r_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.147 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.124 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2331 Nucleic Acid Atoms 82 Solvent Atoms 171 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing