Experiment: 6NPQ

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	8.8	298	31% PEG 3350, 250 mM MgCl2, 125 mM Tris-HCl, 2 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.879	α = 90
b = 57.677	β = 112.74
c = 68.778	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	RAYONIX MX340-HS		2018-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.3	SLAC LCLS	MFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	coMESH	injection

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1		0.3

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1		10	5	9.5

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Total Frames
1	21834

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	1.55	20.13	99.9	0.962	0.196	60.5	50.5		60075			18.38

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	1.55	1.57	99.8		0.16	0.862		6.3

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	3NON	1.55	20.13	1.34	59628	2002	99.93	0.1604	0.1595	0.1865	27.69

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	12.8924
f_angle_d	0.7765
f_chiral_restr	0.0484
f_plane_restr	0.0054
f_bond_d	0.0046

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3368
Nucleic Acid Atoms
Solvent Atoms	298
Heterogen Atoms

Software

Software
Software Name	Purpose
cctbx.xfel	data reduction
cctbx.prime	data scaling
PHENIX	refinement

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.