Experiment: 2NX2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	18 % PEG-4K, Na-Acetate pH 4.6, Ammonium Acetate 0.1M, 0.1M, Ethylene Glycol 10%, Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.052	α = 90
b = 51.052	β = 90
c = 138.22	γ = 90

Symmetry
Space Group	P 41 21 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	MAR CCD 165 mm			M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD	MAR CCD 165 mm			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X3A	0.9793	NSLS	X3A
2	SYNCHROTRON	NSLS BEAMLINE X29A	1.7403	NSLS	X29A
3	SYNCHROTRON	APS BEAMLINE 31-ID	0.979	APS	31-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
1,2,3	2	50	99.9	0.09	26.5	12.6	13121	13121

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	100		0.441	0.91	2.95	5.4	1260

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	2	47.89	13060	637	99.98	0.182	0.18	0.224	RANDOM	25.497

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]
0.54			0.54		-1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.9
r_dihedral_angle_4_deg	15.558
r_dihedral_angle_3_deg	14.7
r_dihedral_angle_1_deg	6.112
r_scangle_it	3.206
r_scbond_it	2.036
r_mcangle_it	1.449
r_angle_refined_deg	1.308
r_mcbond_it	0.857
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.9
r_dihedral_angle_4_deg	15.558
r_dihedral_angle_3_deg	14.7
r_dihedral_angle_1_deg	6.112
r_scangle_it	3.206
r_scbond_it	2.036
r_mcangle_it	1.449
r_angle_refined_deg	1.308
r_mcbond_it	0.857
r_nbtor_refined	0.306
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.181
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1505
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building

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.