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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-TTTT DNA conjugate at 3.12 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 MES monohydrate pH 6.5, 1.6 M Magnesium sulfate heptahydrate
Crystal Properties Matthews coefficient Solvent content 3.58 65.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.759 α = 90 b = 124.759 β = 90 c = 137.221 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 3.12 92.31 100 0.378 0.404 0.142 0.994 6.9 14.8 19914
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) 3.12 3.34 100 2.175 2.332 0.839 0.541 1.4 14.7
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 3.121 88.374 19870 1001 99.859 0.225 0.2247 0.2247 0.2325 0.2324 67.773
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] -3.449 -3.449 6.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.727 r_dihedral_angle_3_deg 14.011 r_dihedral_angle_6_deg 13.598 r_lrange_it 7.576 r_dihedral_angle_1_deg 6.753 r_scangle_it 4.947 r_mcangle_it 4.661 r_scbond_it 2.91 r_mcbond_it 2.774 r_angle_refined_deg 1.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.727 r_dihedral_angle_3_deg 14.011 r_dihedral_angle_6_deg 13.598 r_lrange_it 7.576 r_dihedral_angle_1_deg 6.753 r_scangle_it 4.947 r_mcangle_it 4.661 r_scbond_it 2.91 r_mcbond_it 2.774 r_angle_refined_deg 1.337 r_nbtor_refined 0.309 r_nbd_refined 0.219 r_symmetry_nbd_refined 0.194 r_symmetry_xyhbond_nbd_refined 0.188 r_xyhbond_nbd_refined 0.112 r_ncsr_local_group_1 0.098 r_chiral_restr 0.057 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4576 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction Aimless data scaling PHASER phasing