Experiment: 6WHP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FTG	top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A
experimental model	PDB	4R78	top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A
experimental model	PDB	3MES	top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A
experimental model	PDB	3DXQ	top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A
experimental model	PDB	4DA5	top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A
experimental model	PDB	2PPQ	top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A
experimental model	PDB	2QG7	top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A
experimental model	PDB	3FEG	top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A
experimental model	PDB	3C5I	top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A
experimental model	PDB	1NW1	top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	290	Microlytic/Anatrace MCSG-1 screen, condition D7: 100mM sodium citrate tribasic / citric acid pH 5.5, 20% (w/V) PEG 3350: CrneC.00459.a.B2.PW38290 at 21.6mg/ml: cryo: 20% EG: tray: 293589d7, puck hek5-8

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.5	α = 90
b = 129.5	β = 90
c = 160.01	γ = 120

Symmetry
Space Group	H 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	RAYONIX MX-300		2017-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.25	50	96.6	0.048	0.052	1	24.84	6.429		23840			50.374

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	2.25	2.31	98.2		0.56	0.608	0.871	3.27	6.402

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A	2.25	40.98	1.37	23835	1853	96.58	0.1847	0.1812	0.18	0.2259	0.23	0	51.17

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
f_dihedral_angle_d	17.6467
f_angle_d	0.8315
f_chiral_restr	0.0513
f_bond_d	0.0071
f_plane_restr	0.0065

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3361
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	15

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MR-Rosetta	phasing
Coot	model building

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.