8OZ3 | pdb_00008oz3

Crystal structure of scFv ATOR 1017 bound to human 4-1BB

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2UZI
experimental model	PDB	7YXU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		293	1.1 M sodium/potassium tartrate and 0.1 M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.923	α = 90
b = 125.214	β = 90
c = 128.785	γ = 90

Symmetry
Space Group	P 2 21 21

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-F		2023-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.992	MAX IV	BioMAX

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	3.1	89.8	100	0.997	7.5	11.7		18851

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	3.1	3.31			1

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 (All)	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	3.1	89.776	18809	915	99.942	0.208	0.2047	0.22	0.2708	0.28	RANDOM	130.402

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]
-11.3			13.769		-2.469

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.577
r_lrange_other	18.577
r_dihedral_angle_3_deg	17.416
r_dihedral_angle_6_deg	17.181
r_dihedral_angle_2_deg	16.62
r_scangle_it	15.127
r_scangle_other	15.126
r_mcangle_it	13.319
r_mcangle_other	13.317
r_scbond_it	10.502
r_scbond_other	10.5
r_mcbond_it	9.145
r_mcbond_other	9.144
r_dihedral_angle_1_deg	5.666
r_angle_refined_deg	1.332
r_angle_other_deg	0.461
r_symmetry_nbd_refined	0.222
r_symmetry_nbd_other	0.217
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.203
r_nbd_other	0.18
r_nbtor_refined	0.176
r_ncsr_local_group_3	0.159
r_symmetry_xyhbond_nbd_refined	0.142
r_ncsr_local_group_2	0.139
r_symmetry_xyhbond_nbd_other	0.137
r_ncsr_local_group_1	0.085
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5463
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
autoXDS	data reduction
autoXDS	data scaling
PHASER	phasing