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Glutarate L-2-hydroxylase Q184C, K270A 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 10 % v/v Glycerol, 0.05 M MES pH 5.5, 1.5 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.193 α = 90 b = 96.193 β = 90 c = 184.675 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 4M 2024-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967697 ESRF MASSIF-3
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 1.77 42.66 99.4 0.17 0.176 0.046 0.998 13.5 27.7 42265
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 1.77 1.81 99.4 1.588 1.643 0.421 0.864 2.6 28.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.77 42.66 40151 2107 99.26 0.17476 0.17309 0.1865 0.20508 0.2111 RANDOM 29.993
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] 4.04 4.04 -8.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.077 r_long_range_B_refined 21.012 r_dihedral_angle_3_deg 12.687 r_rigid_bond_restr 12.268 r_scbond_it 10.709 r_mcangle_it 9.897 r_mcbond_it 6.876 r_dihedral_angle_1_deg 6.63 r_angle_refined_deg 1.84 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.077 r_long_range_B_refined 21.012 r_dihedral_angle_3_deg 12.687 r_rigid_bond_restr 12.268 r_scbond_it 10.709 r_mcangle_it 9.897 r_mcbond_it 6.876 r_dihedral_angle_1_deg 6.63 r_angle_refined_deg 1.84 r_chiral_restr 0.124 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2342 Nucleic Acid Atoms 82 Solvent Atoms 234 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing