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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-AAATTT DNA conjugate at 3.15 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 3.48 64.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.556 α = 90 b = 123.556 β = 90 c = 135.898 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 3.15 135.9 100 0.498 0.516 0.134 0.996 8.6 27.1 18850
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) 3.15 3.37 100 3.411 3.53 0.907 0.577 1.3 28.5
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.15 87.52 18800 943 99.809 0.224 0.2225 0.2225 0.2556 0.2556 91.101
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] -2.964 -2.964 5.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.435 r_lrange_it 18.063 r_dihedral_angle_3_deg 16.881 r_dihedral_angle_6_deg 15.538 r_scangle_it 13.92 r_mcangle_it 13.358 r_scbond_it 9.59 r_mcbond_it 9.269 r_dihedral_angle_1_deg 6.766 r_angle_refined_deg 1.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.435 r_lrange_it 18.063 r_dihedral_angle_3_deg 16.881 r_dihedral_angle_6_deg 15.538 r_scangle_it 13.92 r_mcangle_it 13.358 r_scbond_it 9.59 r_mcbond_it 9.269 r_dihedral_angle_1_deg 6.766 r_angle_refined_deg 1.916 r_nbtor_refined 0.313 r_symmetry_nbd_refined 0.249 r_nbd_refined 0.242 r_symmetry_xyhbond_nbd_refined 0.237 r_xyhbond_nbd_refined 0.172 r_ncsr_local_group_1 0.146 r_chiral_restr 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4638 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction Aimless data scaling PHASER phasing