8OGG | pdb_00008ogg

Crystal structure of FutA after an accumulated dose of 5 kGy

X-RAY DIFFRACTION

---

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
2.13	42.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.718	α = 90
b = 78.66	β = 97.788
c = 48.382	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	294	PIXEL	DECTRIS PILATUS3 6M		2018-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.968	Diamond	I24

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.76	40.97	100	0.931	0.923	0.235	3.1	26.23		29256

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.76	1.79			0.93	0.431	0.684	0.41	19.1

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-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.76	40.97	29256	1503	99.956	0.204	0.2017	0.2413	0.2377	31.339

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]
0.187		-0.219	-0.089		-0.037

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.678
r_dihedral_angle_4_deg	14.817
r_dihedral_angle_3_deg	14.53
r_dihedral_angle_1_deg	6.515
r_lrange_other	5.95
r_lrange_it	5.948
r_scangle_it	4.547
r_scangle_other	4.546
r_mcangle_it	2.889
r_mcangle_other	2.889
r_scbond_it	2.835
r_scbond_other	2.834
r_mcbond_it	1.871
r_mcbond_other	1.862
r_angle_refined_deg	1.413
r_angle_other_deg	1.202
r_symmetry_nbd_refined	0.22
r_nbd_other	0.201
r_nbd_refined	0.185
r_symmetry_nbd_other	0.178
r_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.15
r_metal_ion_refined	0.106
r_symmetry_xyhbond_nbd_refined	0.1
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.059
r_ext_dist_refined_d	0.029
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2462
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	1

Software

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