Experiment: 2EB4

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	7% PEG 12000, 0.1M MES, 0.7M potassium thiocyanate, 7% PEG 550 MME, 10mM DTT, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.74	α = 90
b = 136.74	β = 90
c = 192.882	γ = 90

Symmetry
Space Group	P 43 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	RIGAKU JUPITER 210		2006-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.00	SPring-8	BL38B1

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	1.6	50	93.3	0.069	17.9	6.2		223282

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)
	1.6	1.66	68.4		0.406		2.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.6	20	223282	211972	11170	93.34	0.20725	0.20611	0.2287	RANDOM	26.347

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]
0.23			0.23		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.114
r_dihedral_angle_4_deg	16.279
r_dihedral_angle_3_deg	13.223
r_dihedral_angle_1_deg	5.319
r_scangle_it	2.283
r_scbond_it	1.335
r_angle_refined_deg	1.118
r_mcangle_it	0.931
r_mcbond_it	0.483
r_symmetry_vdw_refined	0.388

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.114
r_dihedral_angle_4_deg	16.279
r_dihedral_angle_3_deg	13.223
r_dihedral_angle_1_deg	5.319
r_scangle_it	2.283
r_scbond_it	1.335
r_angle_refined_deg	1.118
r_mcangle_it	0.931
r_mcbond_it	0.483
r_symmetry_vdw_refined	0.388
r_nbtor_refined	0.302
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.113
r_xyhbond_nbd_refined	0.104
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10248
Nucleic Acid Atoms
Solvent Atoms	1008
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

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.