Experiment: 6YA9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EK4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	0.21 M sodium formate, 0.1 M Bis-Tris-Propane buffer pH 8.5, 18% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.64	66.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.43	α = 90
b = 119.43	β = 90
c = 96.62	γ = 90

Symmetry
Space Group	P 41 21 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	PIXEL	DECTRIS PILATUS 2M		2020-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000029	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.15	44.82	99.9	0.999	18.7	19.2		38514			52

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	2.15	2.2	100		0.746		15

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	MOLECULAR REPLACEMENT	THROUGHOUT	3EK4	2.15	44.82	36685	1828	99.83	0.1889	0.1868	0.231	RANDOM	52.208

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]
0.35			0.35		-0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.061
r_dihedral_angle_4_deg	18.911
r_dihedral_angle_3_deg	16.162
r_dihedral_angle_1_deg	6.987
r_angle_refined_deg	1.735
r_angle_other_deg	1.329
r_chiral_restr	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.061
r_dihedral_angle_4_deg	18.911
r_dihedral_angle_3_deg	16.162
r_dihedral_angle_1_deg	6.987
r_angle_refined_deg	1.735
r_angle_other_deg	1.329
r_chiral_restr	0.073
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3190
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	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 R01GM133198.