Experiment: 3EBC

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	290.15	22% PEG 4000, 0.1M imidazole buffer, 0.2M NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.551	α = 90
b = 91.571	β = 107.46
c = 70.594	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	100	CCD	ADSC QUANTUM 315	mirrors	2007-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.0	ALS	5.0.3

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	2.55	43.56	96.1	0.093	0.093	1.9	3.4	18533	17810		-3	28.7

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)
	2.55		96.1		0.313	1.9	3.4	18532

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	2.55	43.56	1.9	18533	17791	858	100	0.28	0.195	0.191	0.279	RANDOM	27.531

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]
-1.53		-0.58	0.33		0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.492
r_dihedral_angle_3_deg	17.755
r_dihedral_angle_4_deg	17.545
r_dihedral_angle_1_deg	5.811
r_scangle_it	1.937
r_angle_refined_deg	1.38
r_scbond_it	1.178
r_mcangle_it	0.987
r_mcbond_it	0.564
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.492
r_dihedral_angle_3_deg	17.755
r_dihedral_angle_4_deg	17.545
r_dihedral_angle_1_deg	5.811
r_scangle_it	1.937
r_angle_refined_deg	1.38
r_scbond_it	1.178
r_mcangle_it	0.987
r_mcbond_it	0.564
r_nbtor_refined	0.315
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_refined	0.176
r_symmetry_hbond_refined	0.169
r_chiral_restr	0.088
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3890
Nucleic Acid Atoms	567
Solvent Atoms	301
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling

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.