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Crystal structure of anti-FX 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 Sodium acetate trihydrate [NaAcet], 20.0 %w/v Polyethylene glycol 3350 [PEG 3350]
Crystal Properties Matthews coefficient Solvent content 2.21 44.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.89 α = 90 b = 62.298 β = 105.55 c = 81.636 γ = 90
Symmetry Space Group C 1 2 1
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 6M 2021-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
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 1.186 49.558 93.5 0.036 0.0406 0.0183 0.999 11.42 4.74 104460
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) 1.186 1.289 57.2 0.9668 1.0688 0.4519 0.61 1.44 5.51 5226
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 1.186 49.56 104460 5168 78.8 0.2069 0.2059 0.1987 0.2265 0.2183 RANDOM 28.15
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] -0.1801 -0.1325 0.14 0.0401
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.31 t_omega_torsion 4.37 t_angle_deg 1.04 t_bond_d 0.008 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 3167 Nucleic Acid Atoms Solvent Atoms 467 Heterogen Atoms 116
Software Software Software Name Purpose autoPROC data processing Aimless data scaling STARANISO data scaling PHENIX refinement XDS data reduction PHASER phasing BUSTER refinement