9EQV | pdb_00009eqv

41fs pulse duration 10uJ pulse energy thaumatin

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	4AXR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	100 mg of thaumatin (Sigma-T7638) was dissolved in 1 ml of MiniQ water, reaching a concentration of 100 mg/ml with solutions vortexed to ensure complete dissolution. Subsequently, 200 uL of the thaumatin solution was mixed with 200 ul of 1.6 M (Na, K, tartrate) crystallization solution

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.5	α = 90
b = 58.5	β = 90
c = 151.25	γ = 90

Symmetry
Space Group	P 41 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	PSI JUNGFRAU 8M		2023-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SwissFEL ARAMIS BEAMLINE ESC	1.0306	SwissFEL ARAMIS	ESC

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	polymer fixed target	fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1		polymer fixed target

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	41 (fs)	100	7.98	12.03 (KeV)

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	13546		13546

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	1.48	32	100	0.95	0.181	4.26	122.2		45753

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	1.48	1.51	100		0.357	1.405	0.71

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	1.48	32	45653	2304	99.967	0.168	0.1667	0.1752	0.2005	0.2046	22.136

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]
0.325			0.325		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	26.155
r_lrange_other	25.645
r_dihedral_angle_6_deg	15.534
r_dihedral_angle_3_deg	12.768
r_dihedral_angle_2_deg	8.847
r_dihedral_angle_1_deg	6.754
r_scangle_it	5.278
r_scangle_other	5.278
r_scbond_other	3.416
r_scbond_it	3.414
r_mcangle_other	3.026
r_mcangle_it	3.016
r_mcbond_it	2.055
r_mcbond_other	2.022
r_angle_refined_deg	1.722
r_angle_other_deg	0.604
r_xyhbond_nbd_refined	0.376
r_symmetry_nbd_refined	0.337
r_symmetry_xyhbond_nbd_refined	0.318
r_nbd_refined	0.296
r_nbd_other	0.27
r_symmetry_nbd_other	0.233
r_symmetry_xyhbond_nbd_other	0.225
r_nbtor_refined	0.187
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1545
Nucleic Acid Atoms
Solvent Atoms	332
Heterogen Atoms	10

Software

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