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Human prion protein (PrP) fragment 119-231 (G127V M129 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 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 2.79 55.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.076 α = 90 b = 128.076 β = 90 c = 135.642 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 2013-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.3 57.93 88.5 0.103 24.5 4.2 26908
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 1.224 2.7
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 2.3 57.93 24982 1362 88.5 0.2026 0.1999 0.1964 0.2512 0.2443 RANDOM 47.674
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] -0.32 -0.32 -0.32 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.945 r_dihedral_angle_4_deg 22.404 r_dihedral_angle_3_deg 18.233 r_dihedral_angle_1_deg 7.456 r_angle_refined_deg 1.735 r_angle_other_deg 0.867 r_chiral_restr 0.099 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.945 r_dihedral_angle_4_deg 22.404 r_dihedral_angle_3_deg 18.233 r_dihedral_angle_1_deg 7.456 r_angle_refined_deg 1.735 r_angle_other_deg 0.867 r_chiral_restr 0.099 r_bond_refined_d 0.015 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 4037 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction pointless data scaling PHASER phasing