8YX1 | pdb_00008yx1

CD40 in complex with Bleselumab Fab

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6FAX
experimental model	PDB	3Z3K
experimental model	PDB	4M6O

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.565	α = 90
b = 116.002	β = 91.713
c = 121.651	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 PILATUS3 S 6M		2021-12-20	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	2.7	45.56	99.9	0.143	0.059	0.996	12.8	6.8		37822

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	2.7	2.8	100		0.941	0.537	0.824	2.3	6.9

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.7	45.56	37802	1858	99.865	0.207	0.204	0.21	0.2651	0.27	52.149

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]
-1.872		-1.951	2.942		-0.952

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.614
r_dihedral_angle_6_deg	13.886
r_dihedral_angle_2_deg	10.349
r_dihedral_angle_1_deg	8.502
r_lrange_other	5.089
r_lrange_it	5.088
r_scangle_it	3.538
r_scangle_other	3.538
r_mcangle_it	3.262
r_mcangle_other	3.262
r_scbond_it	2.158
r_scbond_other	2.158
r_mcbond_it	2.014
r_mcbond_other	2.013
r_angle_refined_deg	1.56
r_angle_other_deg	0.537
r_nbd_other	0.231
r_symmetry_nbd_other	0.216
r_xyhbond_nbd_refined	0.212
r_nbd_refined	0.202
r_symmetry_nbd_refined	0.184
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.093
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.046
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8812
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms

Software

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