8CYH | pdb_00008cyh

Novel Anti-Mesothelin Antibodies Enable Crystallography of the Intact Mesothelin Ectodo- main and Engineering of Potent, T cell-engaging Bispecific Therapeutics

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4F3F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	Tris (8.0), sodium citrate, Peg3350

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.112	α = 90
b = 124.862	β = 90
c = 302.748	γ = 90

Symmetry
Space Group	I 2 2 2

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		2019-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.97926	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.35	50	98.7	0.149	0.164	0.068	8.4	5.8		17506

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	3.35	3.41	96.1		0.934	1.035	0.438	0.598		5.6

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	4F3F	3.38	44.38	16652	851	97.88	0.2315	0.2296	0.23	0.2676	0.26	RANDOM	118.853

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]
14.26			-6.74		-7.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.672
r_dihedral_angle_4_deg	26.63
r_dihedral_angle_3_deg	19.068
r_dihedral_angle_1_deg	8.609
r_angle_refined_deg	1.14
r_angle_other_deg	1.093
r_chiral_restr	0.032
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.672
r_dihedral_angle_4_deg	26.63
r_dihedral_angle_3_deg	19.068
r_dihedral_angle_1_deg	8.609
r_angle_refined_deg	1.14
r_angle_other_deg	1.093
r_chiral_restr	0.032
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5216
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	28

Software

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