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Human prion protein (PrP) fragment 119-231 (G127V V129 variant) complexed to ICSM 18 (anti-Prp therapeutic antibody) Fab fragment
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 300 5 - 6 mg/mL PrP in 0.4 M and 0.75 M ammonium sulphate, 0.05 M Tris (pH 7.5 and 8.0) were equilibrated over wells containing 0.8 M and 1.5 M ammonium sulphate, 0.1 M Tris (pH 7.5 and 8.0).
Crystal Properties Matthews coefficient Solvent content 2.76 55.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.951 α = 90 b = 127.951 β = 90 c = 135.797 γ = 120
Symmetry Space Group P 63 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 300 PIXEL DECTRIS PILATUS 6M 2014-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 2.5 111 99.4 0.142 0.156 0.063 0.992 10.9 5.9 23111
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 2.5 2.6 99.6 1.059 1.162 0.464 0.609 5.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2W9E 2.5 111 21923 1161 99.03 0.1633 0.1607 0.168 0.2124 0.2133 RANDOM 57.011
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] -0.35 -0.18 -0.35 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 19.432 r_dihedral_angle_3_deg 18.059 r_dihedral_angle_1_deg 7.765 r_angle_refined_deg 1.882 r_angle_other_deg 0.922 r_chiral_restr 0.099 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.025 r_dihedral_angle_4_deg 19.432 r_dihedral_angle_3_deg 18.059 r_dihedral_angle_1_deg 7.765 r_angle_refined_deg 1.882 r_angle_other_deg 0.922 r_chiral_restr 0.099 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4078 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 5
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing