7NT0

Drosophila PGRP-LB Y78F mutant in complex with tracheal cytotoxin (TCT)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	30% v/v 2-Propanol, 100 mM Tris base HCl pH 8.5, 30% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.587	α = 92.113
b = 52.167	β = 105.123
c = 55.579	γ = 111.513

Symmetry
Space Group	P 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 PILATUS3 6M		2019-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.969	Diamond	I24

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	1.8	53.07	97.7	0.084	0.098	0.05	0.998	11.9	6.9		34852

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	1.8	1.84			0.478	0.56	0.289	0.891		6.8

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1OHT	1.8	53.067	34851	1760	97.742	0.146	0.1447	0.1798	19.093

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]
0.659	0.031	-0.431	0.125	-0.47	-0.223

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.466
r_dihedral_angle_3_deg	11.766
r_dihedral_angle_4_deg	11.686
r_dihedral_angle_1_deg	7.175
r_lrange_it	5.587
r_lrange_other	5.555
r_scangle_it	4.383
r_scangle_other	4.382
r_scbond_it	2.907
r_scbond_other	2.906
r_mcangle_it	2.567
r_mcangle_other	2.566
r_mcbond_it	1.911
r_mcbond_other	1.911
r_angle_refined_deg	1.684
r_angle_other_deg	1.479
r_symmetry_nbd_refined	0.333
r_nbd_refined	0.213
r_nbd_other	0.179
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.141
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.083
r_symmetry_xyhbond_nbd_other	0.061
r_ncsr_local_group_1	0.051
r_metal_ion_refined	0.043
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2625
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data reduction
DIALS	data processing
Coot	model building
GDA	data collection
Aimless	data scaling
PHASER	phasing