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Glutarate L-2-hydroxylase N187C mutant-5'-Mal-C6-AGCT 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 Sodium chloride, 0.1 M Potassium chloride, 0.05 M HEPES pH 6.5, 1.9 M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.33 63.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.937 α = 90 b = 124.937 β = 90 c = 127.288 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 X 9M 2023-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
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 2.61 127.29 100 0.373 0.386 0.099 0.997 9.2 28.2 31317
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) 2.61 2.73 100 3.455 3.572 0.907 0.646 1.6 29.6
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 2.61 127.288 31259 1529 99.891 0.198 0.1956 0.2002 0.2397 0.2442 55.189
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] -1.463 -1.463 2.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.625 r_lrange_it 15.574 r_lrange_other 15.561 r_dihedral_angle_3_deg 15.446 r_dihedral_angle_6_deg 15.092 r_scangle_it 15.048 r_scangle_other 15.046 r_scbond_it 13.009 r_scbond_other 12.771 r_mcangle_other 11.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.625 r_lrange_it 15.574 r_lrange_other 15.561 r_dihedral_angle_3_deg 15.446 r_dihedral_angle_6_deg 15.092 r_scangle_it 15.048 r_scangle_other 15.046 r_scbond_it 13.009 r_scbond_other 12.771 r_mcangle_other 11.033 r_mcangle_it 11.032 r_mcbond_it 9.031 r_mcbond_other 9.03 r_dihedral_angle_1_deg 6.539 r_angle_refined_deg 1.739 r_angle_other_deg 0.568 r_nbd_other 0.234 r_symmetry_nbd_other 0.219 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.214 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.138 r_xyhbond_nbd_refined 0.133 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_1 0.081 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4638 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building