Experiment: 2NTY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NTX	PDB ENTRY 2NTX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	293	18%(v/v) Tacsimate(Hampton Research), 4%(w/v) PEG 3350, 0.1M Tris-HCl, pH 7.3, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.25	71.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 211.17	α = 90
b = 211.17	β = 90
c = 81.11	γ = 120

Symmetry
Space Group	P 63

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	MAR CCD 225 mm	MAR CCD 225 mm	2006-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9788	SLS	X10SA

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	3.1	50	99.7	0.16	16.81			37649		-3	56.835

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	3.1	3.2	99.8		0.439	4.2		3374

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2NTX	3.1	24.87	37579	1879	100	0.201	0.199	0.21	0.236	0.24	RANDOM	57.315

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]
0.17	0.09		0.17		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.997
r_dihedral_angle_3_deg	23.701
r_dihedral_angle_4_deg	22.878
r_dihedral_angle_1_deg	6.962
r_scangle_it	3.017
r_scbond_it	2.138
r_angle_refined_deg	1.926
r_mcangle_it	1.147
r_mcbond_it	0.873
r_nbtor_refined	0.33

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7564
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	56

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.