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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-GC 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 1 % w/v Polyethylene glycol monomethyl ether 2,000, 0.1 M HEPES pH 7.0, 1 M Succinic acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.27 62.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.773 α = 90 b = 123.773 β = 90 c = 127.49 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 2.06 127.49 100 0.211 0.219 0.057 0.999 13.2 28.2 61736
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) 2.06 2.11 100 3.136 3.246 0.838 0.714 2 29.3
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 2.06 127.49 61631 3182 99.88 0.199 0.1978 0.2004 0.2193 0.2221 43.212
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] -0.885 -0.885 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.596 r_dihedral_angle_6_deg 14.459 r_dihedral_angle_3_deg 12.934 r_lrange_it 8.856 r_scangle_it 6.818 r_dihedral_angle_1_deg 6.478 r_mcangle_it 4.971 r_scbond_it 4.706 r_mcbond_it 3.522 r_angle_refined_deg 1.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.596 r_dihedral_angle_6_deg 14.459 r_dihedral_angle_3_deg 12.934 r_lrange_it 8.856 r_scangle_it 6.818 r_dihedral_angle_1_deg 6.478 r_mcangle_it 4.971 r_scbond_it 4.706 r_mcbond_it 3.522 r_angle_refined_deg 1.586 r_nbtor_refined 0.31 r_nbd_refined 0.198 r_symmetry_nbd_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.144 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.076 r_ncsr_local_group_1 0.068 r_gen_planes_refined 0.009 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4700 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing