4N9G | pdb_00004n9g

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

X-RAY DIFFRACTION

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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 SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS HAD EXPECTED CONTACT RESIDUES REMOVED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 SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS HAD EXPECTED CONTACT RESIDUES REMOVED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 SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS HAD EXPECTED CONTACT RESIDUES REMOVED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 SCAFFOLD: UNPUBLISHED CRYSTAL STRUCTURE OF UNBOUND SCAFFOLD ALL MODELS HAD EXPECTED CONTACT RESIDUES REMOVED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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.27	0.29516	0.3	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