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Alpha-1-antitrypsin in the cleaved conformation in complex with a conformationally nonselective Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GJV 9C5 Fab alone experimental model PDB 9GGP Cleaved alpha-1-antitrypsin in complex with another antibody
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M sodium HEPES, MOPS
0.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine
40% v/v Glycerol; 20% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.61 52.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.254 α = 90 b = 239.246 β = 90 c = 68.945 γ = 90
Symmetry Space Group P 21 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 R 4M Vertical CRL / horizontal elliptical mirror 2024-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9677 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 2.42 47.83 99.9 0.317 0.332 0.098 0.993 8.5 11.3 74867 35.96
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 2.42 2.47 99.9 3.242 3.388 0.976 0.326 11.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.42 47.65 1.33 74695 3827 99.66 0.2132 0.2114 0.2114 0.2472 0.2472 50.41
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 13.2459 f_angle_d 0.5717 f_chiral_restr 0.0426 f_plane_restr 0.004 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12002 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing