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Structure of a mouse IgG antibody fragment that binds Inosine, an RNA modification
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DQT High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 293 50 mM TRIS PH 8.3, 15% PEG 4000, 0.1 mM EDTA
Crystal Properties Matthews coefficient Solvent content 2.31 46.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.817 α = 83.84 b = 49.09 β = 88.82 c = 57.385 γ = 89.68
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 PILATUS3 S 6M 2023-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 1.94 57.04 96.2 0.1901 0.2027 0.06938 0.991 6.33 7.1 30888 26.61
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 1.94 2.009 91.25 1.506 1.642 0.6427 0.586 3.17 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 1.94 57.04 1.96 30805 1554 96.2 0.2064 0.2043 0.2043 0.2453 0.2454 random selection 32.66
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.4893 f_angle_d 1.0987 f_chiral_restr 0.068 f_plane_restr 0.0087 f_bond_d 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3268 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement autoPROC data processing Aimless data scaling PHASER phasing Coot model building autoPROC data reduction