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HyHEL10 Fab complexed with hen egg lysozyme carrying arginine cluster in framework region of light chain.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D9A 3D9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG 400, sodium citrate tribasic dihydrate, Tris hydrochloride
Crystal Properties Matthews coefficient Solvent content 3.44 64.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.9 α = 90 b = 147.9 β = 90 c = 137.7 γ = 120
Symmetry Space Group P 63 2 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 X 9M 2020-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
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 3.13 19.8 99.35 0.09 0.128 0.09 0.987 8.86 2 16124 75.34
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 3.13 3.24 99.94 0.5747 0.8127 0.5747 0.545 1.08 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3D9A 3.13 19.8 1.35 16119 806 99.93 0.2314 0.2296 0.2351 0.2669 0.2725 66.54
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 9.247 f_angle_d 0.8835 f_chiral_restr 0.053 f_plane_restr 0.0061 f_bond_d 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4172 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement