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Glutarate L-2-hydroxylase N187C mutant-5'-Mal-C6-TTTT DNA conjugate
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 3.29 62.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.656 α = 90 b = 124.656 β = 90 c = 126.553 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 EIGER2 XE CdTe 16M 2024-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976254 MAX IV BioMAX
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 2.86 126.55 97 0.392 0.407 0.108 0.992 11.5 26.3 23007
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) 2.86 3.01 100 5.89 6.11 1.621 0.55 1.4 27.2
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 2.86 126.55 22976 1068 97.007 0.216 0.2144 0.2147 0.2524 0.2528 61.15
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] 0.982 0.982 -1.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.449 r_lrange_it 15.148 r_scangle_it 13.984 r_dihedral_angle_6_deg 13.676 r_dihedral_angle_3_deg 13.507 r_scbond_it 11.042 r_mcangle_it 10.554 r_mcbond_it 8.334 r_dihedral_angle_1_deg 5.706 r_angle_refined_deg 1.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.449 r_lrange_it 15.148 r_scangle_it 13.984 r_dihedral_angle_6_deg 13.676 r_dihedral_angle_3_deg 13.507 r_scbond_it 11.042 r_mcangle_it 10.554 r_mcbond_it 8.334 r_dihedral_angle_1_deg 5.706 r_angle_refined_deg 1.328 r_nbtor_refined 0.307 r_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.201 r_symmetry_nbd_refined 0.19 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4628 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building