2F2L | pdb_00002f2l

Crystal structure of tracheal cytotoxin (TCT) bound to the ectodomain complex of peptidoglycan recognition proteins LCa (PGRP-LCa) and LCx (PGRP-LCx)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S2J	pdb entries 1S2J and 1Z6I
experimental model	PDB	1Z6I	pdb entries 1S2J and 1Z6I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	4.2	298	20% polyethylene glycol 1500, 5% ethylene glycol, and 100 mM phosphate-citrate, pH 4.2, EVAPORATION, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.123	α = 90
b = 79.695	β = 90
c = 114.389	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	110	CCD	CUSTOM-MADE		2005-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97950	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.05	50	98	0.088		5.9	24185	23701	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	90.2		0.497	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	pdb entries 1S2J and 1Z6I	2.1	30	22645	21203	1148	98.55	0.16872	0.16872	0.1663	0.22	0.21378	0.26	RANDOM	19.17

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]
1.01			-2.05		1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.928
r_dihedral_angle_4_deg	18.863
r_dihedral_angle_3_deg	13.694
r_dihedral_angle_1_deg	5.917
r_scangle_it	2.226
r_scbond_it	1.417
r_angle_refined_deg	1.329
r_angle_other_deg	0.798
r_mcangle_it	0.674
r_mcbond_it	0.524
r_symmetry_vdw_other	0.251
r_nbd_refined	0.193
r_nbd_other	0.181
r_nbtor_refined	0.177
r_symmetry_vdw_refined	0.177
r_symmetry_hbond_refined	0.172
r_xyhbond_nbd_refined	0.16
r_mcbond_other	0.111
r_nbtor_other	0.084
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2653
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	115

Software

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