Experiment: 2O8E

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	290	11% PEG 8000, 10 mM magnesium sulfate, 100 mM bis-tris-propane, pH 7, VAPOR DIFFUSION, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 257.51	α = 90
b = 257.51	β = 90
c = 257.51	γ = 90

Symmetry
Space Group	P 43 3 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	MARMOSAIC 300 mm CCD	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.005	APS	22-ID

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	3.3	91.044	98.9	0.096	0.096	6.6	9.1	43653	43653		-3

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	3.3	3.39	99.7		0.461	0.461	1.6	7.7	3211

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2O8B	3.3	20	43392	2219	98.47	0.255	0.253	0.291	103.516

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	23.021
r_dihedral_angle_4_deg	12.695
r_dihedral_angle_3_deg	10.969
r_dihedral_angle_1_deg	2.375
r_angle_refined_deg	1.367
r_scangle_it	1.079
r_scbond_it	0.614
r_mcangle_it	0.527
r_nbtor_refined	0.315
r_mcbond_it	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.021
r_dihedral_angle_4_deg	12.695
r_dihedral_angle_3_deg	10.969
r_dihedral_angle_1_deg	2.375
r_angle_refined_deg	1.367
r_scangle_it	1.079
r_scbond_it	0.614
r_mcangle_it	0.527
r_nbtor_refined	0.315
r_mcbond_it	0.297
r_symmetry_hbond_refined	0.25
r_nbd_refined	0.184
r_xyhbond_nbd_refined	0.182
r_symmetry_vdw_refined	0.155
r_chiral_restr	0.096
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13939
Nucleic Acid Atoms	610
Solvent Atoms	10
Heterogen Atoms	28

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
REFMAC	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.