Experiment: 6QYK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LOF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	284	25% PEG3350, 0.2M MAGNESIUM FORMATE, 1MM MALTOSE

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.545	α = 90
b = 133.748	β = 90
c = 37.338	γ = 90

Symmetry
Space Group	P 21 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 PILATUS3 S 6M		2017-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.25	28.9	98.7	0.098	7.9	3.9		23650

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.31	95.6		0.275	2.9	4.1

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	5lof	2.3	15	21048	1149	98.36	0.2213	0.2188	0.2663	RANDOM	41.087

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]
2.16			-5.63		3.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.811
r_dihedral_angle_4_deg	21.26
r_dihedral_angle_3_deg	18.147
r_dihedral_angle_1_deg	5.328
r_angle_refined_deg	1.751
r_angle_other_deg	1.064
r_chiral_restr	0.103
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.811
r_dihedral_angle_4_deg	21.26
r_dihedral_angle_3_deg	18.147
r_dihedral_angle_1_deg	5.328
r_angle_refined_deg	1.751
r_angle_other_deg	1.064
r_chiral_restr	0.103
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3965
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
XSCALE	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 R01GM157729.