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Probing the N-terminal beta-sheet conversion in the crystal structure of the human prion protein bound to a Nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.1 M HEPES-Na pH 7, 15% PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.857 α = 90 b = 45.781 β = 96.23 c = 45.092 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 2010-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 1.0000 ESRF BM30A
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 1.5 65.54 98.8 0.058 13.8 4 42399 42399 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 97.8 0.24 0.24 2.8 4.1 6092
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2W9E 1.5 24.93 42305 2137 98.34 0.1514 0.1497 0.1843 0.2054 RANDOM 16.7219
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] 0.03 0.01 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.402 r_sphericity_free 19.241 r_dihedral_angle_4_deg 17.118 r_dihedral_angle_3_deg 11.78 r_sphericity_bonded 9.22 r_dihedral_angle_1_deg 6.228 r_rigid_bond_restr 5.529 r_mcangle_it 2.972 r_mcbond_it 2.578 r_mcbond_other 2.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.402 r_sphericity_free 19.241 r_dihedral_angle_4_deg 17.118 r_dihedral_angle_3_deg 11.78 r_sphericity_bonded 9.22 r_dihedral_angle_1_deg 6.228 r_rigid_bond_restr 5.529 r_mcangle_it 2.972 r_mcbond_it 2.578 r_mcbond_other 2.573 r_angle_refined_deg 1.939 r_angle_other_deg 0.892 r_chiral_restr 0.123 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1810 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction