Experiment: 1NYK

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	297	Peg 4000, Tris, magnesium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.02	45.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.569	α = 90
b = 78.267	β = 90
c = 136.794	γ = 90

Symmetry
Space Group	C 2 2 21

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	Flat mirror (vertical focusing)	2001-04-20	M	MAD
2	1	x-ray		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.7373, 1.3776, 1.7415	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.965	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	24	98.8		4.2		74518	1.4	1.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.31	1.37	90.4

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	1.31	24	74518	74518	3722	93.4	0.1592	0.1592	0.1576	0.2125	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
	2301	2668.5

RMS Deviations
Key	Refinement Restraint Deviation
s_angle_d	0.03
s_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2310
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	11

Software

Software
Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MOSFLM	data reduction
CCP4	data scaling
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.