8CXC | pdb_00008cxc

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	4F33

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	tris 8.0, zinc chloride, ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
5.37	77.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 185.303	α = 90
b = 204.175	β = 90
c = 123.114	γ = 90

Symmetry
Space Group	C 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		2019-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	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	4.25	50	84.7	0.121	0.151	0.088	12.6	2.6		13542

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	4.25	4.32	85.5		0.784	0.979	0.576	0.263		2.5

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	4f33	4.31	45.78	12857	667	83.95	0.2463	0.2435	0.24	0.2997	0.29	RANDOM	263.302

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]
-5.08			-7.25		12.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.942
r_dihedral_angle_3_deg	18.432
r_dihedral_angle_4_deg	16.47
r_dihedral_angle_1_deg	7.863
r_angle_refined_deg	1.908
r_angle_other_deg	1.166
r_chiral_restr	0.06
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.942
r_dihedral_angle_3_deg	18.432
r_dihedral_angle_4_deg	16.47
r_dihedral_angle_1_deg	7.863
r_angle_refined_deg	1.908
r_angle_other_deg	1.166
r_chiral_restr	0.06
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6984
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

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.