1ZU8 | pdb_00001zu8

Crystal structure of the goat signalling protein with a bound trisaccharide reveals that Trp78 reduces the carbohydrate binding site to half

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	VAPOR DIFFUSION, HANGING DROP	7.8	298	25mM Tris HCl, 50mM NaCl, 19% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.204	α = 90
b = 66.689	β = 90
c = 108.072	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	2005-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	3.05	56	98.6	0.14	7.7			9023			36.7

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	3.05	3.16	99.8		0.425	2

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QZO	3.05	56	9023	8590	433	98.61	0.196	0.19554	0.19346	0.23583	RANDOM	35.895

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]
0.99			-1.06		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.79
r_scangle_it	5.703
r_scbond_it	3.468
r_mcangle_it	2.936
r_dihedral_angle_1_deg	2.616
r_angle_refined_deg	2.316
r_mcbond_it	1.562
r_angle_other_deg	1.344
r_nbtor_other	0.284
r_nbd_refined	0.269
r_nbd_other	0.265
r_symmetry_vdw_other	0.231
r_symmetry_vdw_refined	0.23
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.153
r_xyhbond_nbd_other	0.065
r_symmetry_hbond_refined	0.034
r_bond_refined_d	0.027
r_gen_planes_refined	0.014
r_gen_planes_other	0.006
r_bond_other_d	0.004
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	2877
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	81

Software

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