Experiment: 7R6W

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7JX3	PDB entry 7JX3 and homology model of S2X35 Fab

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	1.85 M ammonium sulfate, 0.1 M Tris, pH 8.17, 0.8% w/v polyvinyl alcohol, 1% v/v 1-propanol, 0.01 M HEPES, pH 7

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.267	α = 90
b = 239.372	β = 90
c = 129.806	γ = 90

Symmetry
Space Group	C 2 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	100	PIXEL	DECTRIS PILATUS 6M		2021-01-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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	1.83	39.52	99.6	0.085	0.092	0.035	0.999	16.2	6.7		144449

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	1.83	1.86	99.5		2.96	3.199	1.202	0.306		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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 7JX3 and homology model of S2X35 Fab	1.83	38.91	135667	7049	98.28	0.2123	0.2113	0.2316	RANDOM	37.283

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]
1.59			-0.13		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.757
r_dihedral_angle_4_deg	16.847
r_dihedral_angle_3_deg	12.067
r_dihedral_angle_1_deg	7.34
r_angle_refined_deg	1.259
r_angle_other_deg	1.154
r_chiral_restr	0.046
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.757
r_dihedral_angle_4_deg	16.847
r_dihedral_angle_3_deg	12.067
r_dihedral_angle_1_deg	7.34
r_angle_refined_deg	1.259
r_angle_other_deg	1.154
r_chiral_restr	0.046
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8160
Nucleic Acid Atoms
Solvent Atoms	584
Heterogen Atoms	172

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
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.