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Anti-tumor antibody 14F7-derived single chain fragment variable (scFv)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, 0.02 M 1,6-hexandiol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 0.1 M bicine/tris base pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.53 51.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.798 α = 90 b = 119.066 β = 90.22 c = 68.286 γ = 90
Symmetry Space Group P 1 21 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 S 6M 2017-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0332 ESRF ID29
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 2.2 46.71 94.8 0.112 0.137 0.078 0.989 3.4 2.5 49026 37.78
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 2.28 96.4 0.532 0.653 0.374 0.8 1.2 2.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3UMT 2.2 46.708 1.33 48584 2495 93.98 0.1865 0.1836 0.1869 0.2384 0.2413 Random
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 15.792 f_angle_d 1.065 f_chiral_restr 0.065 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7194 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection EDNA data collection XDS data reduction PHENIX phasing