Experiment: 3EBE

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	294	PEG 4000, TRIS, KSCN, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.565	α = 90
b = 94.414	β = 112.79
c = 69.775	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	110	CCD	MARMOSAIC 300 mm CCD		2007-03-10	M	SINGLE WAVELENGTH
2	1	x-ray	110	CCD	MARMOSAIC 300 mm CCD		2006-06-10	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID
2	SYNCHROTRON	APS BEAMLINE 22-ID	1.0388, 1.0311, 1.0370	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.3	50	99.6	0.074	27.7	6.7		29404			48.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.3	2.38	97		0.425	2.3	3.9	2882

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.3	44.4	28929	1481	99.73	0.2046	0.2046	0.2023	0.2471	RANDOM	55.685

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]
-1.65		-0.73	0.71		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.584
r_dihedral_angle_4_deg	20.488
r_dihedral_angle_3_deg	20.026
r_dihedral_angle_1_deg	6.919
r_scangle_it	2.973
r_scbond_it	1.814
r_angle_refined_deg	1.572
r_mcangle_it	1.369
r_mcbond_it	0.781
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.584
r_dihedral_angle_4_deg	20.488
r_dihedral_angle_3_deg	20.026
r_dihedral_angle_1_deg	6.919
r_scangle_it	2.973
r_scbond_it	1.814
r_angle_refined_deg	1.572
r_mcangle_it	1.369
r_mcbond_it	0.781
r_nbtor_refined	0.304
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.214
r_symmetry_hbond_refined	0.186
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.123
r_metal_ion_refined	0.042
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4123
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	3

Software

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

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.