Experiment: 3EB5

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	291	0.4 M NH4(SO4)2, 1 M LiSO4, 0.1 M Na Citrate, pH 6.2, vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.869	α = 90
b = 66.474	β = 90
c = 77.465	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	RIGAKU RAXIS IV		2006-09-22	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	1.2827,1.1808,1.2829	SSRL	BL9-2
2	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	28.689	100	0.052	0.052	9.135	9.2	6417	6383

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2	2.11	99.9		0.757	0.757	1	8.9	902

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	28.69	6376	628	99.92	0.219	0.213	0.2181	0.275	0.2743	RANDOM	64.506

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]
0.98			-0.77		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.335
r_dihedral_angle_3_deg	17.299
r_dihedral_angle_4_deg	11.287
r_dihedral_angle_1_deg	4.971
r_scangle_it	2.168
r_angle_refined_deg	1.514
r_scbond_it	1.312
r_mcangle_it	0.918
r_mcbond_it	0.483
r_nbtor_refined	0.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.335
r_dihedral_angle_3_deg	17.299
r_dihedral_angle_4_deg	11.287
r_dihedral_angle_1_deg	4.971
r_scangle_it	2.168
r_angle_refined_deg	1.514
r_scbond_it	1.312
r_mcangle_it	0.918
r_mcbond_it	0.483
r_nbtor_refined	0.318
r_nbd_refined	0.295
r_symmetry_hbond_refined	0.224
r_symmetry_vdw_refined	0.134
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.102
r_metal_ion_refined	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	509
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	3

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

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.