Experiment: 3DON

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	277	0.1M tri-Sodium Citrate dihydrate pH 5.8, 24% PEG 4000, 0.2M Ammonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.877	α = 90
b = 54.153	β = 90
c = 102.724	γ = 90

Symmetry
Space Group	P 21 21 21

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++		2008-01-05	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4r		2008-03-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	0.97901, 0.97953, 0.96429	Photon Factory	BL-6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	47.9	97.9	0.1	5.9	5.57		17458

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)
1,2	2.1	2.18	98.8		0.334	2	5.82	1714

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.1	15	17384	896	97.85	0.187	0.183	0.26	RANDOM	23.175

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]
-0.42			1.19		-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.263
r_dihedral_angle_4_deg	16.643
r_dihedral_angle_3_deg	15.869
r_dihedral_angle_1_deg	6.307
r_scangle_it	3.776
r_scbond_it	2.656
r_mcangle_it	1.75
r_angle_refined_deg	1.723
r_mcbond_it	1.111
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.263
r_dihedral_angle_4_deg	16.643
r_dihedral_angle_3_deg	15.869
r_dihedral_angle_1_deg	6.307
r_scangle_it	3.776
r_scbond_it	2.656
r_mcangle_it	1.75
r_angle_refined_deg	1.723
r_mcbond_it	1.111
r_nbtor_refined	0.3
r_xyhbond_nbd_refined	0.29
r_symmetry_hbond_refined	0.209
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.204
r_chiral_restr	0.134
r_bond_refined_d	0.02
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2084
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	6

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
SOLVE	phasing

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.