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Crystal structure of engineered anti-EE scFv antibody fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NN8 PDB ENTRY 3NN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277.15 Crystals of 3D5/EE_48.K (7.5mg/ml in HBS) were grown at 4 C with 0.1M Tris pH 8.5, 0.2M Li2(SO4), 3% 6-aminohexanoic acid, 24% PEG 8000; crystals appeared in 4-5 days, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.74 55.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.265 α = 90 b = 92.257 β = 110.86 c = 142.708 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 MARMOSAIC 300 mm CCD 2012-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.71 46.1 100 11.85 11363 11363 1.37
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.71 3.84 82.24 0.2206 4.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3NN8 3.71 46.1 1.37 11280 11280 551 0.2645 0.2645 0.2636 0.2692 0.282 0.2861 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 14.32 f_angle_d 0.867 f_chiral_restr 0.031 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7232 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MAR345 data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling