Experiment: 9GWT

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		solved structure of Fab-10F6 alone used as a serch model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	Sodium Cacodylate 0.1M, Glycerol 10% (v/v), NaCl 1M, PEG 600 30.0% (w/v)

Crystal Properties
Matthews coefficient	Solvent content
4.32	71.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.654	α = 90
b = 98.654	β = 90
c = 279.55	γ = 90

Symmetry
Space Group	P 41 21 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 EIGER2 S 16M		2022-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	.999	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.887	93.031	94.3	0.998	16.3	25.1		27539

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.887	3.077			0.618

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.89	93.03	26177	1362	86.02	0.2036	0.2018	0.2026	0.236	0.2341	RANDOM	108.553

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]
0.82			0.82		-1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.8
r_dihedral_angle_1_deg	7.171
r_mcangle_it	3.119
r_dihedral_angle_2_deg	1.955
r_mcbond_it	1.867
r_mcbond_other	1.866
r_angle_refined_deg	0.951
r_angle_other_deg	0.577
r_chiral_restr	0.045
r_bond_other_d	0.021

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.8
r_dihedral_angle_1_deg	7.171
r_mcangle_it	3.119
r_dihedral_angle_2_deg	1.955
r_mcbond_it	1.867
r_mcbond_other	1.866
r_angle_refined_deg	0.951
r_angle_other_deg	0.577
r_chiral_restr	0.045
r_bond_other_d	0.021
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4845
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	234

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
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.