Experiment: 6Y4C

X-RAY DIFFRACTION

Serial Crystallography (SX)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EYM

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	Crystals were grown on an XtalTool support (Jena Bioscience) over a 24 well VDX-plate with 1 ml reservoir. The drop consisted of 1 microlitre 20 mg/ml protein in 10 mM sodium phosphate pH 7.4, 100 mM NaCl, 10 mM beta-mercaptoethanol, 2 mM lactose), 0.25 microlitre of seed crystals in a stabilization solution containing 0.1 M Tris pH 7.5, 33% (w/v) PEG 4000, 0.1 M MgCl2, 0.2 M NaSCN) and 0.75 microlitre reservoir solution containing 0.1 M Tris pH 7.5, 30% PEG 4000, 0.05 M MgCl2, 0.2 M NaSCN and 8 mM beta-mercaptoethanol.

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.03

Symmetry
Space Group	P 21 21 21

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	DECTRIS EIGER X 16M		2019-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9800	MAX IV	BioMAX

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	XtalTool (Jena Bioscience)	fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	Crystallized directly on XtalTool	SPINE pin		MD3 (Arinax)

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	undefined (fs)			undefined (KeV)

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	15555		15555

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	1.7	60	99.9	0.9589303	0.141	5.66	139		15552			17.8

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	1.7	1.75			0.7462656	0.37	2.5

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 (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	6EYM	1.7	42.91	15137	1525	97.47	0.1484	0.1448	0.1591	0.1806	0.1887	RANDOM	22.1

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	13.7632
f_angle_d	0.8772
f_chiral_restr	0.0611
f_bond_d	0.0072
f_plane_restr	0.0059

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1103
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	24

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

6Y4C | pdb_00006y4c