Experiment: 2YVM

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.05M MES, 0.08M MAGNESIUM ACETATE, 7%(W/V) PEG8000, 10%(W/V) GLYCEROL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.763	α = 90
b = 101.176	β = 90
c = 97.492	γ = 90

Symmetry
Space Group	C 2 2 21

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 QUANTUM 210		2004-10-28	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU JUPITER 210		2004-11-17	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	1.0000	SPring-8	BL44B2
2	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.03985, 1.03940, 1.00000	SPring-8	BL26B2

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	1.7	50	99.9	0.044	48	7		22707		-3	15.3

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)
1,2	1.7	1.76	99.8		0.239	7	6.5

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	1.7	25.99	22599	20354	2245	99.9	0.205	0.225	RANDOM	19.1

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]
6.03			-2.14		-3.89

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.8
c_scangle_it	2.33
c_mcangle_it	1.66
c_angle_deg	1.6
c_scbond_it	1.53
c_improper_angle_d	1.14
c_mcbond_it	1
c_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1437
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	2

Software

Software
Software Name	Purpose
MLPHARE	phasing
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.