9QXW | pdb_00009qxw

SSX structure of Thaumatin grown in batch conditions

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	BATCH MODE	6.5	294	Thaumatin from Thaumatococcus danielii (T7639, Sigma-Aldrich) was dissolved in milliQ water to a final concentration of 50 mg/mL. Thaumatin solution was mixed in a 1:1 ratio with a precipitant solution containing 40% (w/v) sodium potassium tartrate, 0.1 M bis-Tris propane pH 6.5 in a 1 mL Eppendorf tube at 21 degrees before vortexing for 10 seconds.

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.97	α = 90
b = 58.97	β = 90
c = 152.55	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	35295	28964	35295

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	1.68	58.97	100	0.987	0.115	6.4	412.89		31714			22.56

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	1.68	1.71	100		0.425	1.701		265.02

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	1.68	55.064	31628	1554	99.994	0.17	0.1686	0.1923	0.1819	29.58

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]
-2.341			-2.341		4.682

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.406
r_lrange_other	18.299
r_scangle_it	14.927
r_scangle_other	14.924
r_dihedral_angle_6_deg	14.552
r_dihedral_angle_3_deg	10.906
r_scbond_it	10.399
r_scbond_other	10.394
r_mcangle_other	10.16
r_mcangle_it	10.144
r_rigid_bond_restr	7.799
r_mcbond_it	7.281
r_mcbond_other	7.202
r_dihedral_angle_1_deg	6.846
r_dihedral_angle_2_deg	5.783
r_angle_refined_deg	1.218
r_angle_other_deg	0.445
r_symmetry_nbd_refined	0.254
r_nbd_other	0.237
r_symmetry_nbd_other	0.194
r_nbd_refined	0.184
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.105
r_symmetry_xyhbond_nbd_refined	0.084
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.065
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
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