9D3Y | pdb_00009d3y

Crystal structure of the catalytic region of human MASP-2 with specific inhibitor Compound S2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q3X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	1.0 uL of protein (0.62 mg/mL MASP2) was mixed with 1.0 uL of reservoir solution (0.1 M Tris-HCl pH 7.8, 0.16 M NaCl, 31% (w/v) PEG 6000, 10% (v/v) glycerol, and 200 uM Compound S2) and equilibrated against reservoir at 20 C. Crystals were cryoprotected in reservoir supplemented with 20% (v/v) glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.77	α = 90
b = 41.05	β = 98.01
c = 102.92	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER X 9M		2023-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95355	CLSI	08ID-1

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	2.08	35.67	99.55	0.1555	0.993	6.44	3.7		18318

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	2.08	2.154			1.545	0.348	1.1

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.08	35.67	18312	951	99.57	0.2066	0.2073	0.261	0.2617

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2429
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	69

Software

Software
Software Name	Purpose
xia2	data reduction
xia2	data scaling
PHASER	phasing
PHENIX	refinement

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.