2A3Y | pdb_00002a3y

Pentameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LGN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	294	sodium actetate, calcium acetate, PEG 8000, PEG 400, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.715	α = 90
b = 69.956	β = 97.09
c = 101.367	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 QUANTUM 4	Double crystal	2003-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.115872	ALS	8.3.1

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	50.7	94.5	0.047	0.047	17.9	2.2	84221	84221	-3	-3	18.1

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	2.07	91.8		0.172	0.172	6.3	2.1	8126

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	1LGN	2	50.6	84201	79985	4216	94.49	0.21738	0.21738	0.21567	0.22	0.24965	0.25	RANDOM	12.732

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]
-1.22		0.2	-1.11		2.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.955
r_scangle_it	3.169
r_scbond_it	2.226
r_mcangle_it	1.321
r_angle_refined_deg	1.086
r_mcbond_it	0.735
r_symmetry_vdw_refined	0.191
r_nbd_refined	0.173
r_symmetry_hbond_refined	0.086
r_xyhbond_nbd_refined	0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.955
r_scangle_it	3.169
r_scbond_it	2.226
r_mcangle_it	1.321
r_angle_refined_deg	1.086
r_mcbond_it	0.735
r_symmetry_vdw_refined	0.191
r_nbd_refined	0.173
r_symmetry_hbond_refined	0.086
r_xyhbond_nbd_refined	0.078
r_chiral_restr	0.071
r_metal_ion_refined	0.018
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8245
Nucleic Acid Atoms
Solvent Atoms	478
Heterogen Atoms	75

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	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 R01GM157729.