9QXY | pdb_00009qxy

SSX structure of Thaumatin grown in microfluidic droplets

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	7AC3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROFLUIDIC	6.5	294	Crystals were grown in a droplet microfluidic device 50 x 40 micron (w x h) with a QX200 oil flow rate of 22.5 uL/min, a crystallisation condition flow rate of 6 uL/min and a thaumatin flow rate of 1.5 uL/min resulting in 81 pL droplets. Thaumatin from Thaumatococcus danielii (T7639, Sigma-Aldrich) was dissolved in milliQ water to a final concentration of 50 mg/mL The crystallisation condition was 40% (w/v) sodium potassium tartrate, 0.1 M bis-Tris propane pH 6.5.

Crystal Properties
Matthews coefficient	Solvent content
2.99	59.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.97	α = 90
b = 58.97	β = 90
c = 152.75	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 4M		2025-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.072	ESRF	ID29

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	SOS Chip	fixed target

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	19053	17659	19053

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	1.6	58.97	100	0.99	0.095	7.1	224.12		36626			20.93

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	1.6	1.63	100		0.314	2.024	0.5	94.16

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	1.6	55.073	36538	1860	100	0.147	0.1457	0.1465	0.1758	0.18	29.453

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]
-2.105			-2.105		4.21

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.626
r_lrange_other	19.619
r_scangle_other	17.214
r_scangle_it	17.213
r_dihedral_angle_6_deg	15.867
r_scbond_it	12.155
r_scbond_other	12.155
r_dihedral_angle_3_deg	11.35
r_mcangle_other	10.735
r_mcangle_it	10.714
r_mcbond_it	7.808
r_mcbond_other	7.752
r_dihedral_angle_1_deg	6.979
r_rigid_bond_restr	6.709
r_dihedral_angle_2_deg	6.297
r_angle_refined_deg	1.677
r_angle_other_deg	0.612
r_symmetry_xyhbond_nbd_refined	0.261
r_symmetry_nbd_refined	0.198
r_symmetry_nbd_other	0.196
r_nbd_refined	0.194
r_nbtor_refined	0.175
r_nbd_other	0.17
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.01
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	1546
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	10

Software

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