Experiment: 6PK8

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	0.15 M Ammonium sulfate, 0.1 M MES pH 6.0, 15% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.6	α = 90
b = 105.26	β = 90
c = 176.53	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	PIXEL	DECTRIS EIGER X 16M		2018-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.91	90.41	98.1	0.171	0.198	0.988	6.67	3.73		25041	-3		46.195

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.91	2.99	89.8		0.975	1.144	0.481	1.17	3.475

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	5GS3	2.91	90.41	22537	2504	98.03	0.1909	0.1856	0.2379	RANDOM	52.733

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]
-1.19			2.44		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.001
r_dihedral_angle_3_deg	18.475
r_dihedral_angle_4_deg	17.265
r_dihedral_angle_1_deg	6.86
r_angle_refined_deg	1.616
r_angle_other_deg	1.279
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.001
r_dihedral_angle_3_deg	18.475
r_dihedral_angle_4_deg	17.265
r_dihedral_angle_1_deg	6.86
r_angle_refined_deg	1.616
r_angle_other_deg	1.279
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6789
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

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.