Experiment: 8BEY

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WA1	3WA1, 5FOY, 5G37
experimental model	PDB	5FOY	3WA1, 5FOY, 5G37
experimental model	PDB	5G37	3WA1, 5FOY, 5G37

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	IN CELL	7	298	Natural

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.65	α = 90
b = 83.11	β = 90
c = 156.91	γ = 90

Symmetry
Space Group	P 21 21 21

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	AGIPD		2022-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	EUROPEAN XFEL BEAMLINE SPB/SFX	1.33	European XFEL	SPB/SFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.62	24.98	100	0.997	10.61	1028.3		132750

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.62	1.64			0.133

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3WA1, 5FOY, 5G37	1.62	24.98	125990	6673	99.95	0.1771	0.1762	0.19	0.1947	0.2	RANDOM	31.465

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]
-0.05			-0.05		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.824
r_dihedral_angle_4_deg	18.028
r_dihedral_angle_3_deg	13.112
r_dihedral_angle_1_deg	7.371
r_angle_refined_deg	1.439
r_angle_other_deg	1.354
r_chiral_restr	0.068
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.824
r_dihedral_angle_4_deg	18.028
r_dihedral_angle_3_deg	13.112
r_dihedral_angle_1_deg	7.371
r_angle_refined_deg	1.439
r_angle_other_deg	1.354
r_chiral_restr	0.068
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6748
Nucleic Acid Atoms
Solvent Atoms	480
Heterogen Atoms

Software

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