2A3X

Decameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy- 2-methyl-1,3-dioxane]- 5-yloxycarbonyl}-piperazine

X-RAY DIFFRACTION

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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 acetate, calcium acetate, PEG 8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.861	α = 90
b = 95.054	β = 98.74
c = 164.257	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		2003-12-19	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	3	59.8		0.071	0.071	14.4	3.2	45367	45367	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.11	85.3		0.349	2.2	2.9

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 (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	3	50	43001	42996	2298	95	0.23087	0.22815	0.21	0.28223	0.26	RANDOM	11.892

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]
3.74		1.08	-3.66		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.674
r_dihedral_angle_1_deg	5.495
r_scbond_it	4.351
r_mcangle_it	2.557
r_mcbond_it	1.643
r_angle_refined_deg	1.074
r_symmetry_vdw_refined	0.193
r_nbd_refined	0.182
r_metal_ion_refined	0.155
r_xyhbond_nbd_refined	0.113
r_symmetry_hbond_refined	0.113
r_chiral_restr	0.101
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16490
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	116

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing