8YX9

CD40 in complex with Dacetuzumab Fab

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.2 M Ammonium citrate tribasic pH 7.0 20% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
3.78	67.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 199.194	α = 90
b = 208.172	β = 90
c = 198.061	γ = 90

Symmetry
Space Group	C 2 2 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 PILATUS3 S 6M		2022-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.8	49.8	100	0.151	0.042	0.999	17.3	13.7		101033

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.85	100		1.35	0.375	0.813	2.1	13.8

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	49.8	100999	4995	99.974	0.212	0.209	0.2617	67.037

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]
3.065			-4.423		1.359

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.748
r_dihedral_angle_6_deg	13.796
r_lrange_it	9.786
r_lrange_other	9.785
r_dihedral_angle_1_deg	7.866
r_mcangle_it	7.383
r_mcangle_other	7.383
r_scangle_it	7.048
r_scangle_other	7.048
r_dihedral_angle_2_deg	6.196
r_mcbond_it	4.769
r_mcbond_other	4.767
r_scbond_it	4.494
r_scbond_other	4.493
r_angle_refined_deg	1.377
r_angle_other_deg	0.475
r_xyhbond_nbd_refined	0.249
r_nbd_refined	0.204
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.179
r_nbd_other	0.158
r_symmetry_nbd_refined	0.121
r_symmetry_xyhbond_nbd_other	0.112
r_symmetry_xyhbond_nbd_refined	0.102
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.061
r_chiral_restr_other	0.054
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16768
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing