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Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C2-GTAC 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 2.8 56.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.699 α = 90 b = 96.699 β = 90 c = 184.671 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 9M 2024-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920194 NSLS-II 17-ID-1
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 1.61 34.5 100 0.134 0.139 0.037 1 18.5 27.2 56851
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 1.61 1.64 100 3.26 3.357 0.891 0.337 27.9
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 1.61 34.5 54030 2821 99.97 0.17473 0.17327 0.1875 0.20029 0.208 RANDOM 34.063
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] -0.65 -0.65 1.3
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 18.993 r_long_range_B_other 18.848 r_dihedral_angle_2_deg 13.525 r_scangle_other 12.481 r_dihedral_angle_3_deg 12.184 r_rigid_bond_restr 11.598 r_scbond_other 8.618 r_scbond_it 8.551 r_mcangle_other 7.51 r_mcangle_it 7.501
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 18.993 r_long_range_B_other 18.848 r_dihedral_angle_2_deg 13.525 r_scangle_other 12.481 r_dihedral_angle_3_deg 12.184 r_rigid_bond_restr 11.598 r_scbond_other 8.618 r_scbond_it 8.551 r_mcangle_other 7.51 r_mcangle_it 7.501 r_dihedral_angle_1_deg 6.164 r_mcbond_it 5.184 r_mcbond_other 5.177 r_angle_refined_deg 1.588 r_angle_other_deg 0.537 r_chiral_restr 0.084 r_gen_planes_other 0.018 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 2371 Nucleic Acid Atoms 82 Solvent Atoms 168 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing