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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-AGCT DNA conjugate at 2.86 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 277.15 25 % v/v Glycerol, 0.05 M Bis-Tris pH 7, 1.4 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.79 67.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.763 α = 90 b = 123.763 β = 90 c = 147.48 γ = 90
Symmetry Space Group P 4 21 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 2023-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920105 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 2.86 147.48 100 0.559 0.621 0.267 0.98 4.8 10 27187
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) 2.86 3.01 100 5.658 6.265 2.67 0.236 0.5 10.3
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.86 147.48 27159 1328 99.967 0.232 0.2301 0.2303 0.2679 0.2661 72.687
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] -2.442 -2.442 4.885
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.656 r_scangle_it 16.242 r_mcangle_it 13.572 r_dihedral_angle_3_deg 12.389 r_scbond_it 12.277 r_dihedral_angle_6_deg 11.855 r_mcbond_it 10.179 r_dihedral_angle_1_deg 6.516 r_dihedral_angle_2_deg 5.267 r_angle_refined_deg 0.991
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.656 r_scangle_it 16.242 r_mcangle_it 13.572 r_dihedral_angle_3_deg 12.389 r_scbond_it 12.277 r_dihedral_angle_6_deg 11.855 r_mcbond_it 10.179 r_dihedral_angle_1_deg 6.516 r_dihedral_angle_2_deg 5.267 r_angle_refined_deg 0.991 r_nbtor_refined 0.304 r_nbd_refined 0.218 r_symmetry_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.204 r_xyhbond_nbd_refined 0.141 r_ncsr_local_group_1 0.088 r_chiral_restr 0.045 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4689 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction Aimless data scaling PHASER phasing