9F7Z | pdb_00009f7z

Crystal structure of human 4-1BB/TNFRSF9 in complex with the anti-4-1BB DARPin protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		proprietary model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.10 M Citric acid pH=5.00 1.60 M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.33	α = 90
b = 102.469	β = 91.54
c = 167.366	γ = 90

Symmetry
Space Group	C 1 2 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		2020-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999953	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.81	167.31	92.4	0.157	0.157	7.1	4.3		47018

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.815	3.173	60.1		1.042	1.042	1.5	4.5

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	2.81	167.31	44690	2328	67.15	0.2436	0.2412	0.2425	0.2912	0.2881	RANDOM	55.416

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]
0.22		-0.16	-0.23		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.615
r_dihedral_angle_4_deg	19.699
r_dihedral_angle_3_deg	16.379
r_dihedral_angle_1_deg	9.028
r_mcangle_it	5.643
r_mcbond_it	3.374
r_mcbond_other	3.373
r_angle_refined_deg	1.55
r_angle_other_deg	1.224
r_chiral_restr	0.057

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.615
r_dihedral_angle_4_deg	19.699
r_dihedral_angle_3_deg	16.379
r_dihedral_angle_1_deg	9.028
r_mcangle_it	5.643
r_mcbond_it	3.374
r_mcbond_other	3.373
r_angle_refined_deg	1.55
r_angle_other_deg	1.224
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15363
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	283

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.