3FLR | pdb_00003flr

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QTJ	Rigid body refinement of polyalanine model of native octameric Limulus SAP, PDB code 1qtj

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	298	Tris, NaCl, pH 7.4, sitting drop, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.33	α = 90
b = 173.33	β = 90
c = 98.81	γ = 90

Symmetry
Space Group	I 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	FILM	CEA		1989-01-01		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX7.2	1.488	SRS	PX7.2

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	3	60.9	89	0.117		4	13666	13666

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)
	3	3.13	55.6		0.284

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	Rigid body refinement of polyalanine model of native octameric Limulus SAP, PDB code 1qtj	3	60.9	13564	674	88.2	0.214	0.214	0.184	0.18	0.232	0.19	Random	30.711

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]
-1.147			-1.147		2.295

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.831
c_mcangle_it	2.156
c_scbond_it	1.768
c_mcbond_it	1.214

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3336
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	4

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
ROTAVATA/AGROVATA	data scaling