Experiment: 3VNF

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	295	0.1M HEPES, pH 7.0, 6% (+/-)-MPD, 15% (w/v) D-(+)-sucrose, VAPOR DIFFUSION, temperature 295K
2	VAPOR DIFFUSION	7	295	0.1M HEPES, pH 7.0, 10% MPD, 1mM DTT, VAPOR DIFFUSION, temperature 295K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.11	α = 90
b = 61.11	β = 90
c = 126.82	γ = 120

Symmetry
Space Group	P 31 2 1

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	ADSC QUANTUM 315		2010-10-30	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC QUANTUM 315		2010-10-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97940	APS	19-ID
2	SYNCHROTRON	APS BEAMLINE 19-ID	0.97940, 0.97951	APS	19-ID

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	1.8	33.03	95.8	0.075	8.3	8.3	25038	23986			53.67

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.8		95.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	2.1	33.03	16617	16550	1326	99.6	0.2368	0.2368	0.2339	0.27	random	77.1694

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]
4.034			4.034		-8.068

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.395
f_angle_d	1.102
f_chiral_restr	0.069
f_bond_d	0.014
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1592
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
d*TREK	data reduction
d*TREK	data scaling
Auto-Rickshaw	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.