8SFG

Crystal Structure of the Open Unbound Catalytically Inactive Makes Caterpillars Floppy-like (MCF) Effector from Vibrio vulnificus CMCP6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6II6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	292	Protein: 8.4 mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3; Screen: AmSO4 Suite (B3), 0.2M Cesium sulfate, 2.2M Ammonium sulfate. Cryo: 1.8M Ammonim sulfate, 25% Succrose

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.381	α = 90
b = 160.661	β = 101.28
c = 71.793	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 300 mm CCD		2019-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.8	30	97.7	0.11	0.11	0.125	0.059	13.3	4.4		32763		-3	54.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.85	94.7		0.751	0.751	0.857	0.411	0.627	1.9	4.3

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	2.8	29.87	31033	1691	97.52	0.1914	0.1893	0.2296	RANDOM	65.041

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]
-0.73		-1.64	1.44		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.522
r_dihedral_angle_4_deg	7.13
r_dihedral_angle_3_deg	6.88
r_dihedral_angle_1_deg	1.541
r_angle_refined_deg	1.203
r_angle_other_deg	0.324
r_chiral_restr	0.055
r_gen_planes_refined	0.053
r_gen_planes_other	0.049
r_bond_refined_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.522
r_dihedral_angle_4_deg	7.13
r_dihedral_angle_3_deg	6.88
r_dihedral_angle_1_deg	1.541
r_angle_refined_deg	1.203
r_angle_other_deg	0.324
r_chiral_restr	0.055
r_gen_planes_refined	0.053
r_gen_planes_other	0.049
r_bond_refined_d	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10130
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	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 R01GM133198.