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Crystal structure of the Apo Antibody fragment (Fab) raised against C-terminal domain of Ebola nucleoprotein (EBOV, TAFV, BDBV strains)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 90 mM imidazole, pH 8.0, 180 mM Zinc Acetate, 27% PEG 3000, 10 mM Chromium (III) chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 2.32 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.621 α = 90 b = 74.621 β = 90 c = 323.695 γ = 90
Symmetry Space Group P 41 2 2
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 210r 2016-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.000 APS 19-BM
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 2.11 47.4 93.7 4.23 6.2 50593 27.8
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 5VKD 2.112 37.31 1.35 50500 1999 93.67 0.2203 0.2183 0.2217 0.2675 0.2687 random selection
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 11.765 f_angle_d 0.681 f_chiral_restr 0.024 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6278 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement HKL-3000 data collection HKL-3000 data processing HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing PHENIX model building