4N9G

Crystal Structure of a Computationally Designed RSV-Presenting Epitope Scaffold And Its Elicited Antibody 17HD9

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q6G	17HD9 N TERMINAL DOMAIN PAIR: PDB ENTRY 3Q6G AND 3EO9. 17HD9 C TERMINAL DOMAIN PAIR: PDB ENTRY 3QHZ AND 3SOB. SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS HAD EXPECTED CONTACT RESIDUES REMOVED
experimental model	PDB	3EO9	17HD9 N TERMINAL DOMAIN PAIR: PDB ENTRY 3Q6G AND 3EO9. 17HD9 C TERMINAL DOMAIN PAIR: PDB ENTRY 3QHZ AND 3SOB. SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS HAD EXPECTED CONTACT RESIDUES REMOVED
experimental model	PDB	3QHZ	17HD9 N TERMINAL DOMAIN PAIR: PDB ENTRY 3Q6G AND 3EO9. 17HD9 C TERMINAL DOMAIN PAIR: PDB ENTRY 3QHZ AND 3SOB. SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS HAD EXPECTED CONTACT RESIDUES REMOVED
experimental model	PDB	3SOB	17HD9 N TERMINAL DOMAIN PAIR: PDB ENTRY 3Q6G AND 3EO9. 17HD9 C TERMINAL DOMAIN PAIR: PDB ENTRY 3QHZ AND 3SOB. SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS HAD EXPECTED CONTACT RESIDUES REMOVED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	14% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.213	α = 89.99
b = 89.266	β = 102.73
c = 104.304	γ = 89.91

Symmetry
Space Group	P 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		2013-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0000	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	48.75	97.7	0.076	9.4	3.9	78170	76354	5	5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	97.5		0.212	4.4	3.89

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	17HD9 N TERMINAL DOMAIN PAIR: PDB ENTRY 3Q6G AND 3EO9. 17HD9 C TERMINAL DOMAIN PAIR: PDB ENTRY 3QHZ AND 3SOB. SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS HAD EXPECTED CONTACT RESIDUES REMOVED	2.5	48.75	76354	72525	3829	97.68	0.26496	0.26496	0.26335	0.29516	RANDOM	41.108

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]
0.14	-0.04	-0.02	-0.02	-0.05	-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.873
r_dihedral_angle_4_deg	15.563
r_dihedral_angle_3_deg	13.612
r_dihedral_angle_1_deg	5.836
r_scangle_it	1.192
r_angle_refined_deg	0.961
r_scbond_it	0.754
r_angle_other_deg	0.74
r_mcangle_it	0.622
r_mcbond_it	0.332
r_chiral_restr	0.055
r_mcbond_other	0.048
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14202
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling