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Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CX5 PDB ENTRY 2CX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.2 M ammonium sulfate, 30% PEG8000, 0.2 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.6 α = 90 b = 80.4 β = 111.9 c = 67.3 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 93 IMAGE PLATE MAR scanner 345 mm plate 2010-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.25 17 98 0.074 12.8 1.57 14573 14246
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.3 99.5 0.339 3.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 2CX5 2.25 17 14495 12879 665 93.4 0.2168 0.2251 0.236 0.2419 RANDOM 24.085
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] 1.527 0.472 -0.551 -0.976
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.012 c_mcangle_it 2.191 c_scbond_it 2.054 c_mcbond_it 1.354
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2275 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 11
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing CNS refinement XDS data reduction XDS data scaling