5LN4 | pdb_00005ln4

Crystal structure of self-complemented PsaA, the major subunit of pH 6 antigen from Yersinia pests, in complex with choline

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LND

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	294	0.1 M imidazole, 0.2 M zinc acetate and 18% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.542	α = 90
b = 44.625	β = 120.36
c = 99.441	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 PILATUS3 6M		2012-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.36	49.4	99.5	0.082	11.2	3.5		25917

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	2.36	2.44	99.6		0.63	1.2	3.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5LND	2.36	49.397	24595	1322	99.41	0.2314	0.2294	0.23	0.2685	0.27	RANDOM	44.315

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]
1.7		1.48	-2.36		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.844
r_dihedral_angle_3_deg	18.439
r_dihedral_angle_4_deg	9.292
r_dihedral_angle_1_deg	8.112
r_mcangle_it	5.489
r_scbond_it	4.667
r_mcbond_it	3.671
r_angle_refined_deg	2.256
r_chiral_restr	0.129
r_bond_refined_d	0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.844
r_dihedral_angle_3_deg	18.439
r_dihedral_angle_4_deg	9.292
r_dihedral_angle_1_deg	8.112
r_mcangle_it	5.489
r_scbond_it	4.667
r_mcbond_it	3.671
r_angle_refined_deg	2.256
r_chiral_restr	0.129
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3116
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	21

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.