Experiment: 6PDN

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	20% PEG3350, 0.1 M bis-tris propane pH8.5, 0.2 M sodium fluoride, 10% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.001	α = 90
b = 98.001	β = 90
c = 80.248	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2018-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9762	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	49.05	100	8.9	10.2		17226

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	100		0.766		10.1

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.4	49.05	16388	833	99.97	0.1902	0.1884	0.2234	RANDOM	43.097

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]
1.17	0.59		1.17		-3.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.59
r_dihedral_angle_4_deg	15.846
r_dihedral_angle_3_deg	12.664
r_dihedral_angle_1_deg	6.632
r_angle_refined_deg	1.323
r_angle_other_deg	1.19
r_chiral_restr	0.06
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.59
r_dihedral_angle_4_deg	15.846
r_dihedral_angle_3_deg	12.664
r_dihedral_angle_1_deg	6.632
r_angle_refined_deg	1.323
r_angle_other_deg	1.19
r_chiral_restr	0.06
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2264
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	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.