Experiment: 2NYI

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Protein solution (10 mg/mL protein, 0.050 M Sodium chloride, 0.0003 M TCEP, 0.005 M MES pH 6.0) mixed in a 1:1 ratio with the well solution (24% PEG 8000, 0.04 M Magnesium chloride, 0.2 M Sodium fluoride, 0.10 M PIPES pH 6.5). Cryoprotection: well solution supplemented with up to 20% ethylene glycol, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.013	α = 90
b = 79.991	β = 111.25
c = 55.53	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-11-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97923, 0.96400	APS	23-ID-D

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	1.8	45.62	96.3	0.071	11.673	7.4		39789

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	1.8	1.84	83.2		0.419	2.656	4.9	2291

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-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.8	45.62	39742	39742	2027	96.021	0.178	0.178	0.176	0.214	RANDOM	27.458

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]
0.248		0.362	0.326		-0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.269
r_dihedral_angle_4_deg	17.258
r_dihedral_angle_3_deg	12.62
r_scangle_it	8.885
r_scbond_it	6.255
r_dihedral_angle_1_deg	5.621
r_mcangle_it	2.677
r_mcbond_it	1.446
r_angle_refined_deg	1.287
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.269
r_dihedral_angle_4_deg	17.258
r_dihedral_angle_3_deg	12.62
r_scangle_it	8.885
r_scbond_it	6.255
r_dihedral_angle_1_deg	5.621
r_mcangle_it	2.677
r_mcbond_it	1.446
r_angle_refined_deg	1.287
r_nbtor_refined	0.299
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.177
r_xyhbond_nbd_refined	0.16
r_symmetry_vdw_refined	0.156
r_chiral_restr	0.096
r_bond_refined_d	0.017
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2589
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction

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.