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Glutarate L-2-hydroxylase N182A, 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 0.15 M Potassium chloride, 25 % v/v Glycerol, 0.05 M Bis-Tris pH 7, 1.6 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.78 55.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.335 α = 90 b = 96.335 β = 90 c = 184.22 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 16M 2024-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979361 NSLS-II 17-ID-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 1.42 34.41 100 0.106 0.114 0.041 0.999 15.9 14.8 81604
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 1.42 1.44 100 1.642 1.798 0.726 0.359 12
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 1.42 34.41 77643 3959 99.99 0.15137 0.15049 0.1488 0.16812 0.1691 RANDOM 23.814
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] -1.62 -1.62 3.23
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 33.506 r_long_range_B_refined 26.972 r_long_range_B_other 23.277 r_dihedral_angle_2_deg 13.608 r_scangle_other 12.926 r_dihedral_angle_3_deg 12.555 r_scbond_it 8.771 r_scbond_other 8.77 r_mcangle_other 8.172 r_mcangle_it 8.119
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 33.506 r_long_range_B_refined 26.972 r_long_range_B_other 23.277 r_dihedral_angle_2_deg 13.608 r_scangle_other 12.926 r_dihedral_angle_3_deg 12.555 r_scbond_it 8.771 r_scbond_other 8.77 r_mcangle_other 8.172 r_mcangle_it 8.119 r_dihedral_angle_1_deg 6.424 r_mcbond_other 5.651 r_mcbond_it 5.556 r_angle_refined_deg 1.434 r_angle_other_deg 0.527 r_chiral_restr 0.078 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d r_dihedral_angle_4_deg 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2332 Nucleic Acid Atoms 82 Solvent Atoms 298 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing