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Crystal structure of anti-FIXa IgG fab without FAST-Ig mutations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20.0 %w/v Polyethylene glycol 3350 [PEG 3350], 0.1 M CBTP buffer [CBTP] pH 6.4
Crystal Properties Matthews coefficient Solvent content 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.937 α = 90 b = 162.082 β = 98.05 c = 139.014 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 4M 2021-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.04500 Photon Factory BL-1A
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 3.192 137.644 86.4 0.521 0.5634 0.2122 0.929 4.1 7.02 18205
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) 3.192 3.705 37.7 1.3761 1.4874 0.5574 0.552 1.64 6.77 911
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5DK3 3.192 42.5 18195 855 61 0.2015 0.196 0.194 0.3098 0.3061 RANDOM 52.42
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] 2.6136 -5.0715 -5.0797 2.4661
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.15 t_omega_torsion 2.84 t_angle_deg 1.16 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12276 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling PHENIX refinement PHASER phasing BUSTER refinement