Experiment: 3EBV

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	298	0.1 M CAPS pH 10.5, 2.0 M Ammonium sulfate, 0.2 M Lithium sulfate, Vapor diffusion, Sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.636	α = 90
b = 96.636	β = 90
c = 124.735	γ = 120

Symmetry
Space Group	H 3

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		2008-07-10		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979	NSLS	X29A

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	1.5	50	99.8	0.088	0.071	22.1	6.2	70137	70137			16.5

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)
	1.5	1.55	99.9		0.454	0.404	4.1	5.8	13903

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		THROUGHOUT	1.5	28.21	70126	3535	99.82	0.157	0.156	0.15	0.169	0.17	RANDOM	16.785

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
r_dihedral_angle_2_deg	35.162
r_dihedral_angle_4_deg	11.632
r_dihedral_angle_3_deg	10.327
r_dihedral_angle_1_deg	5.562
r_scangle_it	3.537
r_scbond_it	2.314
r_mcangle_it	1.515
r_angle_refined_deg	1.463
r_mcbond_it	1.032
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.162
r_dihedral_angle_4_deg	11.632
r_dihedral_angle_3_deg	10.327
r_dihedral_angle_1_deg	5.562
r_scangle_it	3.537
r_scbond_it	2.314
r_mcangle_it	1.515
r_angle_refined_deg	1.463
r_mcbond_it	1.032
r_nbtor_refined	0.308
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.205
r_symmetry_hbond_refined	0.137
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2171
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
CCP4	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.