6SUZ | pdb_00006suz

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)
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	0.17	0.2124	0.21	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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.