1YJO | pdb_00001yjo

Structure of NNQQNY from yeast prion Sup35 with zinc acetate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	293	ZINC SULFATE, SODIUM ACETATE, HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
1.38	10.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 21.153	α = 90
b = 4.87	β = 102.93
c = 23.13	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	MARRESEARCH	ELLIPSOIDAL MIRROR	2004-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13		ESRF	ID13

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	1.3	80	97.1	0.146	9.8	3.8		2166			11.7

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	1.4	88.8		0.426	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.3	22.54	1250	1250	52	97.9	0.103	0.102	0.12	0.152	0.17	RANDOM	5.76

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]
-0.16		0.28	-0.44		0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	59.937
r_dihedral_angle_3_deg	9.092
r_dihedral_angle_1_deg	8.504
r_scangle_it	1.715
r_scbond_it	1.394
r_angle_refined_deg	1.077
r_mcangle_it	0.895
r_angle_other_deg	0.728
r_mcbond_it	0.663
r_symmetry_vdw_other	0.339
r_mcbond_other	0.228
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.219
r_nbtor_refined	0.194
r_nbd_other	0.187
r_symmetry_hbond_refined	0.181
r_symmetry_vdw_refined	0.171
r_chiral_restr	0.092
r_nbtor_other	0.083
r_metal_ion_refined	0.039
r_symmetry_metal_ion_refined	0.016
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_gen_planes_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	55
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	1

Software

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