6SUZ

Human prion protein (PrP) fragment 119-231 (G127V V129 variant) complexed to ICSM 18 (anti-Prp therapeutic antibody) Fab fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W9E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3005 - 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 coefficientSolvent content
2.7655.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.951α = 90
b = 127.951β = 90
c = 135.797γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300PIXELDECTRIS PILATUS 6M2014-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.511199.40.1420.1560.0630.99210.95.923111
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)RedundancyNumber Unique Reflections (All)
12.52.699.61.0591.1620.4640.6095.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2W9E2.511121923116199.030.16330.16070.2124RANDOM57.011
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]
-0.35-0.18-0.351.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.025
r_dihedral_angle_4_deg19.432
r_dihedral_angle_3_deg18.059
r_dihedral_angle_1_deg7.765
r_angle_refined_deg1.882
r_angle_other_deg0.922
r_chiral_restr0.099
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.025
r_dihedral_angle_4_deg19.432
r_dihedral_angle_3_deg18.059
r_dihedral_angle_1_deg7.765
r_angle_refined_deg1.882
r_angle_other_deg0.922
r_chiral_restr0.099
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4078
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms5

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing