Experiment: 2O8F

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O8B	PDB ENTRY 2O8B

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
3.14	60.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 259.55	α = 90
b = 259.55	β = 90
c = 259.55	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	1.00	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	3.25	82.077	99.7	0.129	0.129	4.9	6.6	47220	47220		-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	3.25	3.33	99.8		0.492	0.492	1.6	5.9	3446

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2O8B	3.25	20	47000	2373	99.57	0.246	0.243	0.293	RANDOM	110.542

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	19.558
r_dihedral_angle_3_deg	8.794
r_dihedral_angle_4_deg	7.872
r_dihedral_angle_1_deg	2.009
r_angle_refined_deg	1.198
r_scangle_it	0.51
r_nbtor_refined	0.307
r_mcangle_it	0.298
r_scbond_it	0.285
r_mcbond_it	0.166

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.558
r_dihedral_angle_3_deg	8.794
r_dihedral_angle_4_deg	7.872
r_dihedral_angle_1_deg	2.009
r_angle_refined_deg	1.198
r_scangle_it	0.51
r_nbtor_refined	0.307
r_mcangle_it	0.298
r_scbond_it	0.285
r_mcbond_it	0.166
r_symmetry_hbond_refined	0.163
r_nbd_refined	0.156
r_xyhbond_nbd_refined	0.15
r_symmetry_vdw_refined	0.125
r_chiral_restr	0.089
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13950
Nucleic Acid Atoms	711
Solvent Atoms	19
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 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.