8VM1

Structural Elucidation of the Mesothelin Mucin16 CA125 Interaction

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8CXC
experimental model	PDB	7SA9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	Bis-Tris, NH4CL, PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.203	α = 90
b = 73.237	β = 90
c = 75.054	γ = 90

Symmetry
Space Group	P 21 21 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 6M		2023-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00	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)	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	2.65	50	99	0.066	0.074	0.034	0.992	20.9	5.3		9868

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	2.65	2.7	100		0.628	0.691	0.283	0.822		5.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.65	33.42	9117	480	98.25	0.25049	0.24781	0.29849	RANDOM	80.658

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]
-1.5			1.17		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.779
r_dihedral_angle_4_deg	21.719
r_dihedral_angle_3_deg	17.762
r_long_range_B_other	7.324
r_long_range_B_refined	7.323
r_dihedral_angle_1_deg	7.057
r_scangle_other	6.297
r_mcangle_it	4.553
r_mcangle_other	4.552
r_scbond_it	4.154
r_scbond_other	4.153
r_mcbond_it	3.116
r_mcbond_other	3.102
r_angle_refined_deg	1.551
r_angle_other_deg	1.148
r_chiral_restr	0.059
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1469
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
DENZO	data reduction
PHASER	phasing