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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-TTTT DNA conjugate at 2.02 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 10 % v/v Glycerol, 0.05 M MES pH 5.5, 1.5 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.28 62.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.211 α = 90 b = 124.211 β = 90 c = 127.025 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 2.02 88.81 100 0.22 0.23 0.06 1 9.4 16.5 65331
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 2.02 2.07 100 3.593 3.96 1.04 0.36 0.8 14.1
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 2.023 88.809 65294 3143 99.988 0.213 0.212 0.212 0.2405 0.2405 44.209
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] -1.031 -1.031 2.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.904 r_dihedral_angle_6_deg 14.815 r_dihedral_angle_3_deg 14.07 r_lrange_it 9.14 r_scangle_it 7.324 r_dihedral_angle_1_deg 6.195 r_mcangle_it 5.215 r_scbond_it 5.034 r_mcbond_it 3.706 r_angle_refined_deg 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.904 r_dihedral_angle_6_deg 14.815 r_dihedral_angle_3_deg 14.07 r_lrange_it 9.14 r_scangle_it 7.324 r_dihedral_angle_1_deg 6.195 r_mcangle_it 5.215 r_scbond_it 5.034 r_mcbond_it 3.706 r_angle_refined_deg 1.58 r_nbtor_refined 0.311 r_symmetry_nbd_refined 0.214 r_nbd_refined 0.198 r_symmetry_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.076 r_ncsr_local_group_1 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_metal_ion_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4650 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building