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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-AGCT DNA conjugate at 2.37 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 3.54 65.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.605 α = 90 b = 124.605 β = 90 c = 136.192 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 2023-03-26 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 2.37 37.85 100 0.2 0.2 0.06 1 10.8 13.6 44174
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 2.37 2.46 100 2.584 2.77 0.75 0.67 13.5
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 2.37 37.016 44065 2183 99.765 0.219 0.2173 0.2171 0.2442 0.2464 RANDOM 58.982
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] -0.873 -0.873 1.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.364 r_dihedral_angle_6_deg 14.222 r_dihedral_angle_3_deg 13.064 r_lrange_it 7.429 r_dihedral_angle_1_deg 6.598 r_scangle_it 4.895 r_mcangle_it 4.453 r_scbond_it 2.957 r_mcbond_it 2.718 r_angle_refined_deg 1.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.364 r_dihedral_angle_6_deg 14.222 r_dihedral_angle_3_deg 13.064 r_lrange_it 7.429 r_dihedral_angle_1_deg 6.598 r_scangle_it 4.895 r_mcangle_it 4.453 r_scbond_it 2.957 r_mcbond_it 2.718 r_angle_refined_deg 1.312 r_nbtor_refined 0.307 r_symmetry_xyhbond_nbd_refined 0.213 r_nbd_refined 0.205 r_symmetry_nbd_refined 0.183 r_xyhbond_nbd_refined 0.123 r_ncsr_local_group_1 0.072 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4692 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing Coot model building