Experiment: 3EA4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YBH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.4	291	0.1M CHES, 0.2M Li2SO4, 1M potassium sodium tartrate, 1mM ThDP, 1mM FAD, 1mM MgCl2, 5mM DTT, 1mM MSE , pH 9.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.468	α = 90
b = 178.468	β = 90
c = 184.948	γ = 120

Symmetry
Space Group	P 64 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	CCD	ADSC QUANTUM 4	MIRRORS	2005-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	1.00	APS	14-BM-C

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	2.8	58.42	98.7	0.075	0.075	20.1	5.8	42923	42923

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	2.8	2.9	96.4		0.315	0.315		5.3	4060

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FOURIER SYNTHESIS	THROUGHOUT	1YBH	2.8	58.42	40611	40611	2153	98.53	0.19969	0.19969	0.19895	0.19	0.21348	0.21	RANDOM	52.026

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]
0.19	0.09		0.19		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.918
r_dihedral_angle_4_deg	17.658
r_dihedral_angle_3_deg	15.789
r_dihedral_angle_1_deg	5.36
r_scangle_it	1.492
r_angle_refined_deg	1.153
r_scbond_it	0.846
r_mcangle_it	0.653
r_mcbond_it	0.363
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.918
r_dihedral_angle_4_deg	17.658
r_dihedral_angle_3_deg	15.789
r_dihedral_angle_1_deg	5.36
r_scangle_it	1.492
r_angle_refined_deg	1.153
r_scbond_it	0.846
r_mcangle_it	0.653
r_mcbond_it	0.363
r_nbtor_refined	0.304
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.175
r_symmetry_hbond_refined	0.129
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.077
r_metal_ion_refined	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4456
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	120

Software

Software
Software Name	Purpose
ADSC	data collection
CCP4	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
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.