☰ Navigation Tabs
Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-AGCT DNA conjugate at 1.89 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 2.93 57.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.043 α = 90 b = 97.043 β = 90 c = 185.372 γ = 90
Symmetry Space Group I 4 2 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 2023-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980099 SOLEIL PROXIMA 2
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 1.89 48.52 99.8 0.079 0.082 0.022 1 27.4 26.4 35691
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) 1.89 1.93 97.4 1.467 1.524 0.41 0.776 2.6 25.9
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 1.891 48.52 35690 1758 99.807 0.201 0.2 0.2015 0.2283 0.2318 40.192
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] -0.339 -0.339 0.678
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.156 r_dihedral_angle_3_deg 11.211 r_lrange_it 10.341 r_scangle_it 9.422 r_scbond_it 7.593 r_mcangle_it 7.318 r_dihedral_angle_1_deg 5.913 r_mcbond_it 5.752 r_dihedral_angle_2_deg 5.713 r_angle_refined_deg 1.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.156 r_dihedral_angle_3_deg 11.211 r_lrange_it 10.341 r_scangle_it 9.422 r_scbond_it 7.593 r_mcangle_it 7.318 r_dihedral_angle_1_deg 5.913 r_mcbond_it 5.752 r_dihedral_angle_2_deg 5.713 r_angle_refined_deg 1.149 r_nbtor_refined 0.3 r_metal_ion_refined 0.222 r_nbd_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.148 r_symmetry_nbd_refined 0.138 r_xyhbond_nbd_refined 0.099 r_chiral_restr 0.093 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2365 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling XDS data reduction PHASER phasing