1VFY

PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF VPS27P PROTEIN FROM SACCHAROMYCES CEREVISIAE

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6		0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE PH 4.6, 15% PEG 4000, pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.16	38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.09	α = 111.79
b = 26.57	β = 92.7
c = 31.61	γ = 105.7

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC		1999-02-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B	1.2830,1.2822,1.2320	NSLS	X9B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.15	30	95.4	0.065	0.065	18.6	3.8	21646	20972

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	82.3		0.011	0.011	8	3.4

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.15	30	20972	20972	977	85.4	0.174	0.181	RANDOM	12.6

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]
0.119	0.176	0.537	0.786	1.795	-0.9

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.7
c_scangle_it	4.86
c_scbond_it	3.43
c_mcangle_it	2.2
c_angle_deg	1.77
c_mcbond_it	1.57
c_improper_angle_d	1.03
c_bond_d	0.012
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	532
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement