Experiment: 6QF5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NEF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	0.1M Tris pH 8.5, 0.1M sodium chloride, 0.1M magnesium chloride, 22-25% PEG 400, cadmium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.48	64.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.2	α = 90
b = 122.2	β = 90
c = 94.14	γ = 90

Symmetry
Space Group	P 42

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	CS-PAD XPP		2016-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.3670	SLAC LCLS	MFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Sample Solvent
1	on-chip crystallization	single crystalline silicon chip	aluminum support	Roadrunner II		none, naked crystals

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	60		1	9.07

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Total Frames
1		3377	137476

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	3.7	37.38	99.97	0.783	0.437	2.32	28.1		14866			104.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.7	3.76	99.93		0.105	1.538	0.92	17.7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4NEF	3.7	33.892	1.33	14805	1488	99.13	0.2873	0.2818	0.3357	105.453

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	13.439
f_angle_d	0.761
f_chiral_restr	0.04
f_plane_restr	0.007
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6608
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	3

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
PHASER	phasing
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling

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.