2B31 | pdb_00002b31

Crystal structure of the complex formed between goat signalling protein with pentasaccharide at 3.1 A resolution reveals large scale conformational changes in the residues of TIM barrel

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.8	298	25mM Tris HCl, 50mM NaCl, 19% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0 K, pH 7.80

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.745	α = 90
b = 66.613	β = 90
c = 107.812	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	MARRESEARCH	MIRROR	2005-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300

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	3.1	56.7	98.5	0.11	7			8493

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	3.1	3.21	99.5		0.43	2.4

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QZO	3.1	56.7	8493	8090	403	98.17	0.17859	0.1766	0.21782	RANDOM	24.973

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]
0.4			0.08		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	22.793
r_scangle_it	5.634
r_scbond_it	3.417
r_mcangle_it	3.163
r_angle_refined_deg	2.44
r_angle_other_deg	2.381
r_dihedral_angle_1_deg	2.243
r_mcbond_it	1.683
r_nbtor_other	0.472
r_symmetry_vdw_other	0.409
r_symmetry_vdw_refined	0.311
r_nbd_refined	0.296
r_nbd_other	0.268
r_symmetry_hbond_refined	0.258
r_xyhbond_nbd_refined	0.233
r_xyhbond_nbd_other	0.231
r_chiral_restr	0.152
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.003
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_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	2876
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	98

Software

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