3FLP | pdb_00003flp

Crystal structure of native heptameric SAP-like pentraxin from Limulus polyphemus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Dimer created from A subunit of native octameric Limulus SAP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	298	PEG 6000, CaCl2, MES, pH 7.4, sitting drop, temperature 298.0K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.48	64.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.32	α = 90
b = 167.56	β = 92.5
c = 140.87	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	ADSC		2003-05-06		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1	1.488	SRS	PX14.1

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	2.3	45.27	89.7	0.08	0.08	5.435	2.1	180419	180419

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)
	2.3	2.42	93.2		0.167	0.167	3.9	2	27379

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	Dimer created from A subunit of native octameric Limulus SAP	2.3	45.27	180238	180238	9112	89.4	0.219	0.219	0.201	0.2	0.223	0.22	Random	14.165

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]
-0.867		0.081	0.583		0.284

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.605
c_scbond_it	1.907
c_mcangle_it	1.638
c_mcbond_it	1.03

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23352
Nucleic Acid Atoms
Solvent Atoms	881
Heterogen Atoms	28

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	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.