Experiment: 1YVG

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F82

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	PEG 4000, magnesium chloride, hepes buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.53	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.61	α = 90
b = 177.28	β = 90
c = 54.55	γ = 90

Symmetry
Space Group	C 2 2 2

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	BRANDEIS - B4	Mirrors	2004-05-01	M	MAD
2	1	x-ray	100	CCD	ADSC QUANTUM 315	Mirrors	2004-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	1.2810, 1.2824	NSLS	X12C
2	SYNCHROTRON	NSLS BEAMLINE X25	1.10	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	50	99.4	0.12	7.5	9.4	20639	20639			47

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.49	99.1		7	9.3	2001

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD and Molecular replacement	THROUGHOUT	1F82	2.6	50	15170	15170	1033	92.7	0.2182	0.22	0.2763	0.27	Random	46.6

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]
13.339			20.489		-33.828

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.338
c_mcangle_it	1.918
c_scbond_it	1.488
c_angle_deg	1.36447
c_mcbond_it	1.114
c_bond_d	0.008306

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3222
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	1

Software

Software
Software Name	Purpose
CBASS	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
SHARP	phasing

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.