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Glutarate L-2-hydroxylase N187C mutant-5'-Mal-C6-GC 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 7 295 0.05 M Bis-Tris pH 7, 1.5 M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.27 62.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.083 α = 90 b = 124.083 β = 90 c = 126.932 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 EIGER2 X 9M 2023-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
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 2.06 126.93 100 0.361 0.373 0.096 0.997 8 28.5 61788
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) 2.06 2.11 100 2.992 3.095 0.789 0.601 1.6 29.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.06 126.93 61716 3182 99.934 0.201 0.2003 0.2228 0.2028 35.675
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] -0.36 -0.36 0.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.972 r_dihedral_angle_6_deg 14.508 r_dihedral_angle_3_deg 13.475 r_lrange_it 8.091 r_lrange_other 8.089 r_scangle_it 6.52 r_scangle_other 6.519 r_dihedral_angle_1_deg 6.246 r_scbond_it 4.315 r_scbond_other 4.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.972 r_dihedral_angle_6_deg 14.508 r_dihedral_angle_3_deg 13.475 r_lrange_it 8.091 r_lrange_other 8.089 r_scangle_it 6.52 r_scangle_other 6.519 r_dihedral_angle_1_deg 6.246 r_scbond_it 4.315 r_scbond_other 4.298 r_mcangle_other 4.211 r_mcangle_it 4.21 r_mcbond_it 2.964 r_mcbond_other 2.964 r_angle_refined_deg 1.573 r_angle_other_deg 0.513 r_dihedral_angle_other_2_deg 0.51 r_nbd_other 0.221 r_nbd_refined 0.215 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.151 r_xyhbond_nbd_refined 0.132 r_symmetry_nbd_refined 0.114 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.075 r_ncsr_local_group_1 0.06 r_gen_planes_other 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4601 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building