8CZ8 | pdb_00008cz8

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	9	295	bicine (9.0), glycerol, ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.795	α = 90
b = 83.795	β = 90
c = 230.45	γ = 120

Symmetry
Space Group	P 32

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		2021-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.78652	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.6	50	99.9	0.093	0.988	30.8	4.7		55600

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64			0.697	0.9

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	2.6	45.16	52762	2782	99.75	0.1918	0.19	0.19	0.2241	0.22	RANDOM	67.271

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]
-0.68	-0.34		-0.68		2.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.175
r_dihedral_angle_4_deg	18.178
r_dihedral_angle_3_deg	14.916
r_dihedral_angle_1_deg	6.801
r_angle_refined_deg	1.28
r_angle_other_deg	1.119
r_chiral_restr	0.043
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.175
r_dihedral_angle_4_deg	18.178
r_dihedral_angle_3_deg	14.916
r_dihedral_angle_1_deg	6.801
r_angle_refined_deg	1.28
r_angle_other_deg	1.119
r_chiral_restr	0.043
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9056
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	2427

Software

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