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Glutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-AAATTT DNA conjugate in P 4 21 2 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 3.27 62.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.84 α = 90 b = 123.84 β = 90 c = 127.128 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 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 1.65 34.62 100 0.132 0.14 0.047 0.999 14.4 16.5 118646
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) 1.65 1.68 100 3.414 3.634 1.239 0.356 0.9 16.5
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 1.65 34.62 112806 5800 99.98 0.19285 0.19169 0.1917 0.21535 0.2154 RANDOM 21.777
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] -0.67 -0.67 1.34
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.73 r_dihedral_angle_2_deg 15.559 r_scbond_it 12.808 r_dihedral_angle_3_deg 11.889 r_mcangle_it 10.426 r_mcbond_it 7.497 r_dihedral_angle_1_deg 6.017 r_rigid_bond_restr 5.381 r_angle_refined_deg 1.52 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.73 r_dihedral_angle_2_deg 15.559 r_scbond_it 12.808 r_dihedral_angle_3_deg 11.889 r_mcangle_it 10.426 r_mcbond_it 7.497 r_dihedral_angle_1_deg 6.017 r_rigid_bond_restr 5.381 r_angle_refined_deg 1.52 r_chiral_restr 0.081 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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 4588 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing