7TUM | pdb_00007tum

Multi-Hit SFX using MHz XFEL sources- first hit

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	6FTR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	3.5	293	NaCl, ethylene glycol, PEG 3350, acetate buffer pH 3.5

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.3	α = 90
b = 79.3	β = 90
c = 37.73	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	AGIPD		2017-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	EUROPEAN XFEL BEAMLINE SPB/SFX	1.3332	European XFEL	SPB/SFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	GDVN	undefined (µl/min)	undefined (µm)

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	3.2	35.49	93.6	0.412	4.36	4.55		2072

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	3.2	3.28	90.79		0.638

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6FTR	3.202	35.489	2057	207	93.585	0.325	0.3138	0.3157	0.4262	0.4267	10.88

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]
-0.374			-0.374		0.748

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.657
r_dihedral_angle_3_deg	16.782
r_dihedral_angle_4_deg	15.237
r_dihedral_angle_1_deg	7.569
r_angle_refined_deg	1.447
r_angle_other_deg	1.223
r_rigid_bond_restr	1.166
r_lrange_it	0.889
r_lrange_other	0.889
r_mcangle_other	0.582
r_mcangle_it	0.581
r_scangle_it	0.501
r_scangle_other	0.501
r_mcbond_it	0.403
r_mcbond_other	0.39
r_scbond_other	0.36
r_scbond_it	0.358
r_nbd_other	0.317
r_symmetry_xyhbond_nbd_refined	0.274
r_symmetry_nbd_refined	0.226
r_nbd_refined	0.221
r_symmetry_nbd_other	0.216
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.063
r_symmetry_xyhbond_nbd_other	0.037
r_bond_refined_d	0.005
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
Aimless	data scaling
PHASER	phasing