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Glutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-AAATTT DNA conjugate in I422 space group
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 0.08 M Sodium chloride, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30 % v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 3.37 63.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.996 α = 90 b = 120.996 β = 90 c = 137.384 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 2024-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979338 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 1.64 33.43 100 0.181 0.193 0.066 0.996 10 16.3 62305
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) 1.64 1.67 100 4.584 4.902 1.729 0.26 0.8 15.6
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 1.64 33.427 62304 3057 99.974 0.167 0.1646 0.1658 0.203 0.2052 34.226
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] 3.033 3.033 -6.066
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 30.14 r_scangle_it 28.252 r_scbond_it 21.928 r_mcangle_it 17.455 r_mcbond_it 13.937 r_dihedral_angle_2_deg 13.914 r_dihedral_angle_6_deg 13.884 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_1_deg 5.852 r_rigid_bond_restr 3.885
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 30.14 r_scangle_it 28.252 r_scbond_it 21.928 r_mcangle_it 17.455 r_mcbond_it 13.937 r_dihedral_angle_2_deg 13.914 r_dihedral_angle_6_deg 13.884 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_1_deg 5.852 r_rigid_bond_restr 3.885 r_angle_refined_deg 1.436 r_nbtor_refined 0.306 r_nbd_refined 0.203 r_symmetry_nbd_refined 0.163 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.105 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2298 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing