2ONX | pdb_00002onx

NNQQ peptide corresponding to residues 8-11 of yeast prion sup35 (alternate crystal form)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YJP	pdb entry 1yjp

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	30-50 mg/mL peptide disolved in water and mixed with an equal volume of reservoir solution consisting of 100 mM trisodium citrate, 20% polyethylene glycol 4000 and 20% isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 4.854	α = 90
b = 16.014	β = 96.91
c = 15.546	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	MAR CCD 165 mm		2005-07-16	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 Merge 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	1.5	90	63.8	0.152	10.1	1.5		259			20.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.62	26.1		0.299		1.2	23

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	pdb entry 1yjp	1.52	15.43	251	28	66.05	0.175	0.172	0.19	0.202	0.21	RANDOM	12.236

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]
-1.65		0.39	0.16		1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	49.819
r_dihedral_angle_3_deg	12.152
r_mcangle_it	8.154
r_scangle_it	7.297
r_dihedral_angle_1_deg	6.443
r_scbond_it	5.002
r_mcbond_it	4.914
r_angle_refined_deg	1.314
r_mcbond_other	1.24
r_angle_other_deg	0.926
r_nbd_refined	0.201
r_symmetry_vdw_other	0.178
r_symmetry_hbond_refined	0.17
r_nbd_other	0.165
r_nbtor_refined	0.158
r_chiral_restr	0.148
r_nbtor_other	0.066
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	35
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction