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Glutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-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 0.3 M Lithium sulfate, 0.05 M Bis-Tris pH 7, 18 % w/v PEG 1000
Crystal Properties Matthews coefficient Solvent content 3.33 63.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.414 α = 90 b = 124.414 β = 90 c = 128.175 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 16M 2023-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976284 Diamond I03
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 2.25 64.09 100 0.157 0.163 0.043 0.999 15 26.6 48353
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) 2.25 2.32 100 1.747 1.815 0.493 0.893 2.2 26.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.25 51.091 48054 2347 99.431 0.215 0.2136 0.2138 0.2332 0.2359 RANDOM 48.662
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] -1.071 -1.071 2.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.312 r_dihedral_angle_3_deg 12.119 r_dihedral_angle_2_deg 11.636 r_dihedral_angle_1_deg 6.566 r_lrange_it 5.73 r_scangle_it 3.763 r_mcangle_it 3.118 r_scbond_it 2.232 r_mcbond_it 1.924 r_angle_refined_deg 1.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.312 r_dihedral_angle_3_deg 12.119 r_dihedral_angle_2_deg 11.636 r_dihedral_angle_1_deg 6.566 r_lrange_it 5.73 r_scangle_it 3.763 r_mcangle_it 3.118 r_scbond_it 2.232 r_mcbond_it 1.924 r_angle_refined_deg 1.244 r_nbtor_refined 0.304 r_nbd_refined 0.192 r_symmetry_nbd_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.161 r_xyhbond_nbd_refined 0.147 r_ncsr_local_group_1 0.061 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4660 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing