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Single-chain Fv antibody of F8 complex with NNP-Cap
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K4Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.6 M sodium citrate tribasic dihydrate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.11 41.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.77 α = 90 b = 34.95 β = 99.26 c = 46.21 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 2023-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.88 50 97.1 0.282 4.5 6.7 17379 23.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.99 98 1.924 0.433 0.7 6.7
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 1.88 40.97 1.35 17292 865 96.7 0.2222 0.2207 0.2207 0.2508 0.2509 36.87
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 16.4609 f_angle_d 0.7291 f_chiral_restr 0.0493 f_plane_restr 0.0075 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1782 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing