7XHG | pdb_00007xhg

Crystal structure of the NTF2L domain of human G3BP1 in complex with the Caprin-1 derived peptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FCJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289.15	0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30 % w/v Polyethylene glycol 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.669	α = 90
b = 171.761	β = 99.82
c = 42.968	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS EIGER X 16M		2019-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97915	SSRF	BL17U1

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	2.45	85.88	99.6	0.106	0.126	0.068	0.971	28.2	3.4		21506

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	2.45	2.49			0.532	0.629	0.333	0.818	4.1

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	4fcj	2.46	85.88	20403	1073	99.12	0.2095	0.206	0.21	0.2746	0.27	RANDOM	39.622

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]
3.45		1.11	-2.01		-1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.455
r_dihedral_angle_3_deg	18.245
r_dihedral_angle_4_deg	17.824
r_dihedral_angle_1_deg	7.05
r_angle_refined_deg	1.572
r_angle_other_deg	0.974
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.455
r_dihedral_angle_3_deg	18.245
r_dihedral_angle_4_deg	17.824
r_dihedral_angle_1_deg	7.05
r_angle_refined_deg	1.572
r_angle_other_deg	0.974
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4430
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	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.