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Crystal structure of a Fab variant containing a fluorescent noncanonical amino acid with blocked excited state proton transfer and in complex with its antigen, CD40L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6W9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 16-24% PEG MME 2000, 0.1 M Trimethylamine N-oxide, 0.1 M Tris-HCl pH 7.5-9.0
Crystal Properties Matthews coefficient Solvent content 3.58 65.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 226.847 α = 90 b = 131.252 β = 109.1 c = 97.296 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 CCD ADSC QUANTUM 315r 2017-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.98 ALS 8.2.2
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 2 50 97.8 0.171 0.2 0.104 5.9 3.5 175991
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 2 2.03 97.4 0.551 0.656 0.353 0.702 3.3
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 6w9g 2 48.42 167072 8919 97.61 0.1945 0.1927 0.1993 0.2281 0.2326 RANDOM 23.84
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] -0.09 0.04 0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.55 r_dihedral_angle_4_deg 23.422 r_dihedral_angle_3_deg 15.497 r_dihedral_angle_1_deg 8.165 r_angle_refined_deg 1.869 r_angle_other_deg 1.378 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.55 r_dihedral_angle_4_deg 23.422 r_dihedral_angle_3_deg 15.497 r_dihedral_angle_1_deg 8.165 r_angle_refined_deg 1.869 r_angle_other_deg 1.378 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12733 Nucleic Acid Atoms Solvent Atoms 1276 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing