4OOJ

Crystal structure of the N-terminal domain of the Legionella pneumophila protein SidC at 2.4A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		partial model after phasing and building in AutoSol

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	0.1M sodium cacodylate, 0.2M magnesium chloride, 10% PEG 1000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.1M sodium citrate, 0.2M sodium acetate, 10% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.055	α = 90
b = 119.055	β = 90
c = 201.7	γ = 120

Symmetry
Space Group	P 32

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 PILATUS 6M		2010-10-06	M	SINGLE WAVELENGTH
2	2	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2012-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9786	SLS	X10SA
2	SYNCHROTRON	SLS BEAMLINE X10SA	0.9794	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.4	50	99.8	0.101	0.054	19.03	28.65		124784		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.4	2.5	99.8		0.579	0.473	2.87	28.32

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	partial model after phasing and building in AutoSol	2.4	45.9	124784	6240	100	0.2031	0.2	0.2618	RANDOM	50.024

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]
-2.22	-1.11		-2.22		3.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.63
r_dihedral_angle_4_deg	17.201
r_dihedral_angle_3_deg	16.447
r_dihedral_angle_1_deg	6.764
r_scangle_it	3.974
r_scbond_it	2.436
r_angle_refined_deg	1.669
r_mcangle_it	1.512
r_angle_other_deg	0.978
r_mcbond_it	0.788

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.63
r_dihedral_angle_4_deg	17.201
r_dihedral_angle_3_deg	16.447
r_dihedral_angle_1_deg	6.764
r_scangle_it	3.974
r_scbond_it	2.436
r_angle_refined_deg	1.669
r_mcangle_it	1.512
r_angle_other_deg	0.978
r_mcbond_it	0.788
r_mcbond_other	0.173
r_chiral_restr	0.096
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19440
Nucleic Acid Atoms
Solvent Atoms	419
Heterogen Atoms	123

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
PHENIX	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.