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Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine at pH 9.7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 273 30% PEG 3350, 0.1 M Citric Acid/Sodium Citrate pH 3.8
Crystal Properties Matthews coefficient Solvent content 2.08 40.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.861 α = 90 b = 60.182 β = 98.94 c = 73.258 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 2016-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.91976 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.75 72.37 99 0.153 0.175 0.082 5.3 4.2 39519
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 1.75 1.78 99.5 0.694 0.804 0.4 0.662 3.7
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 6bjz 1.75 72.37 37564 1955 98.77 0.1949 0.1925 0.1995 0.2407 0.2419 RANDOM 29.291
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] 0.79 0.65 -0.01 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.393 r_dihedral_angle_4_deg 17.195 r_dihedral_angle_3_deg 12.152 r_dihedral_angle_1_deg 7.444 r_angle_refined_deg 1.723 r_angle_other_deg 0.973 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.003 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.393 r_dihedral_angle_4_deg 17.195 r_dihedral_angle_3_deg 12.152 r_dihedral_angle_1_deg 7.444 r_angle_refined_deg 1.723 r_angle_other_deg 0.973 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3210 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction