8OEI | pdb_00008oei

SFX structure of FutA after an accumulated dose of 350 kGy

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VP1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		294	Purified protein, diluted crystal seeds, and crystallisation buffer were mixed at a 1:1.5:1.5 ratio. Crystallisation buffer was 25% PEG 3350, 200 mM sodium thiocyanate. Crystal seed stock was diluted 1:20 in 25% PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.366	α = 90
b = 78.22	β = 97.903
c = 48.025	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	MPCCD		2022-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.126	SACLA	BL2

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	Details	Sample Solvent
1	Silicon nitride chip				25600 apertures

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	10 (fs)	30		undefined (KeV)

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	1.65	32.441	100	0.97	0.134	3.7	165.2		34653			20.98

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.679	100		0.691	0.4	0.43	82.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.65	32.441	34653	1786	99.957	0.161	0.1599	0.1599	0.1885	0.1888	27.641

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]
0.295		-0.303	0.161		-0.358

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.86
r_dihedral_angle_3_deg	12.708
r_lrange_it	7.073
r_lrange_other	7.071
r_dihedral_angle_1_deg	6.182
r_scangle_it	6.13
r_scangle_other	6.129
r_dihedral_angle_2_deg	5.619
r_scbond_it	3.834
r_scbond_other	3.831
r_mcangle_it	2.842
r_mcangle_other	2.841
r_mcbond_it	2.019
r_mcbond_other	2.002
r_angle_refined_deg	1.572
r_angle_other_deg	0.538
r_symmetry_nbd_refined	0.277
r_nbd_refined	0.221
r_nbd_other	0.205
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.144
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2460
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
cctbx.xfel.merge	data scaling
MOLREP	phasing