Experiment: 1YGA

CRYSTAL STRUCTURE OF Saccharomyces cerevisiae YN9A PROTEIN, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	290	PEG4000, TRIS-HCL, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.38	49.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.86	α = 90
b = 88.07	β = 90
c = 103.08	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	88	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2004-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2	20	89.4	0.065	0.077	12.1	12.6	44056	44056			11.3

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	48.1		0.24	0.25	2.7	1.8	2328

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MIR	THROUGHOUT	2	20	1	44056	43705	1320	88.8	0.23	0.207	0.207	0.2054	0.229	0.2249	RANDOM	25.6

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]
-7.89			5.66		2.23

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.9
c_scangle_it	4.14
c_scbond_it	2.94
c_mcangle_it	2.8
c_mcbond_it	1.97
c_angle_deg	1.3
c_improper_angle_d	1.16
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5244
Nucleic Acid Atoms
Solvent Atoms	539
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
ARP/wARP	model building
CNS	refinement