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Crystal structure of anti-FIXa IgG fab with 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 0.2 M Calcium chloride dihydrate [CaCl2] , 20.0 %w/v Polyethylene glycol 3350 [PEG 3350]
Crystal Properties Matthews coefficient Solvent content 2.07 40.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.27 α = 90 b = 232.84 β = 93.96 c = 41.432 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 1.79 116.42 91.1 0.1476 0.1632 0.0688 0.994 7.79 5.66 53046
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) 1.79 1.935 60 1.1551 1.2453 0.4646 0.653 1.54 7.18 2189
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 1.79 20.67 53004 2717 72.7 0.2048 0.2012 0.1951 0.2727 0.263 RANDOM 29.49
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] -0.5062 -0.1519 0.2974 0.2088
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.43 t_omega_torsion 3.87 t_angle_deg 1.08 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 6565 Nucleic Acid Atoms Solvent Atoms 775 Heterogen Atoms 112
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling STARANISO data scaling PHENIX refinement PHASER phasing BUSTER refinement