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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-AAATTT DNA conjugate at 2.47 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 3.25 62.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.218 α = 90 b = 123.218 β = 90 c = 127.629 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 2.47 127.63 100 0.382 0.396 0.104 0.998 10.1 27 35919
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) 2.47 2.57 100 4.952 5.132 1.348 0.366 0.9 27.7
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 2.47 127.629 35893 1852 99.997 0.216 0.2146 0.2146 0.2431 0.243 56.964
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] -1.172 -1.172 2.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.343 r_dihedral_angle_6_deg 15.509 r_dihedral_angle_3_deg 15.433 r_lrange_it 15.071 r_scangle_it 14.732 r_scbond_it 13.157 r_mcangle_it 10.342 r_mcbond_it 9.637 r_dihedral_angle_1_deg 6.791 r_angle_refined_deg 1.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.343 r_dihedral_angle_6_deg 15.509 r_dihedral_angle_3_deg 15.433 r_lrange_it 15.071 r_scangle_it 14.732 r_scbond_it 13.157 r_mcangle_it 10.342 r_mcbond_it 9.637 r_dihedral_angle_1_deg 6.791 r_angle_refined_deg 1.742 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.236 r_nbd_refined 0.209 r_symmetry_xyhbond_nbd_refined 0.159 r_xyhbond_nbd_refined 0.144 r_ncsr_local_group_1 0.087 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4597 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building