Experiment: 4YMK

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	6.9	298	35% PEG400, 200 mM sodium chloride, 4% ethylene glycol, 100 mM MES, pH 6.9
2	LIPIDIC CUBIC PHASE	6.9	298	35% PEG400, 200 mM sodium chloride, 4% ethylene glycol, 100 mM MES, pH 6.9

Crystal Properties
Matthews coefficient	Solvent content
4.13	70.2
4.13	70.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.061	α = 90
b = 113.766	β = 90
c = 141.698	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS PILATUS 6M-F		2013-11-18	M	SINGLE WAVELENGTH
2	2	x-ray	93	PIXEL	DECTRIS PILATUS 6M-F		2014-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9795	APS	24-ID-C
2	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.2541	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.6	50	98	0.111	0.121	0.047	0.992	6.9	6.2		38065			43.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64	94		0.53	0.588	0.248	0.827		5	1813

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	SAD	FREE R-VALUE	2.605	47.411	1.36	38016	1999	97.94	0.2044	0.2027	0.2	0.2353	0.23	Random selection	46.8574

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.087
f_angle_d	0.633
f_chiral_restr	0.03
f_bond_d	0.002
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5231
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	188

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data scaling
Aimless	data scaling
SHELXDE	phasing
PHASER	phasing
HKL-2000	data scaling
Coot	model building
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.