2OMM | pdb_00002omm

GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35

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	EVAPORATION, RECRYSTALLIZATION		298	peptide was dissolved at 10 mg/mL in water, quickly filtered, and left to sit at room temperature, EVAPORATION, RECRYSTALLIZATION, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 23.324	α = 90
b = 4.934	β = 90
c = 37.548	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	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	2	19.81	96.4	0.248	4.61			380		-3	2.446

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)
	2	2.2	98.9		0.417	2.7		90

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	2	19.81	372	18	94.66	0.242	0.241	0.24	0.252	0.24	RANDOM	12.533

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]
0.05			0.19		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	56.115
r_dihedral_angle_3_deg	11.183
r_dihedral_angle_1_deg	7.418
r_mcangle_it	3.309
r_mcbond_it	2.691
r_scangle_it	2.561
r_scbond_it	2.295
r_angle_refined_deg	1.544
r_mcbond_other	0.873
r_angle_other_deg	0.635
r_nbd_other	0.18
r_nbtor_refined	0.18
r_symmetry_vdw_other	0.159
r_symmetry_vdw_refined	0.153
r_xyhbond_nbd_refined	0.149
r_nbd_refined	0.123
r_chiral_restr	0.104
r_nbtor_other	0.085
r_symmetry_hbond_refined	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	59
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction