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Crystal structure of engineered CYS-CYS fab dimer VL-108 (LC33)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1% PEG 2000, 100 mM HEPES pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.19 61.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.634 α = 90 b = 99.634 β = 90 c = 212.675 γ = 120
Symmetry Space Group P 31 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 PILATUS 6M 2021-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.99987 ALS 5.0.2
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 2.97 70.89 99.9 0.248 0.262 0.083 0.994 9.8 9.8 17133
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 3.7 3.9 100 0.787 0.829 0.257 0.9 10.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.97 70.89 17133 902 69.46 0.1962 0.1921 0.1831 0.2739 0.2442 RANDOM 78.494
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] 10.81 10.81 -21.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.653 r_dihedral_angle_3_deg 24.353 r_dihedral_angle_4_deg 22.636 r_dihedral_angle_1_deg 8.797 r_angle_refined_deg 1.959 r_angle_other_deg 1.28 r_chiral_restr 0.069 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.653 r_dihedral_angle_3_deg 24.353 r_dihedral_angle_4_deg 22.636 r_dihedral_angle_1_deg 8.797 r_angle_refined_deg 1.959 r_angle_other_deg 1.28 r_chiral_restr 0.069 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6584 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction PHASER phasing