9QQG | pdb_00009qqg

Acoustofluidic Sample Delivery System for Serial Crystallography, Thaumatin with acoustic OFF

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6C5Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		273	100 mg of Thaumatin from Thaumatococcus daniellii (Sigma, T7638) was dissolved in 1 mL of MiliQ 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. A tube of the resulting mixture was placed on a rotator operating at 20 C. After an incubation period of 16-18 hr, thaumatin crystals grow to a size of 15-20 um with high density. Crystals were stored at 4 C until the experiment.

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.65	α = 90
b = 58.65	β = 90
c = 151.75	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	273	PIXEL	DECTRIS EIGER2 X CdTe 9M		2024-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE MicroMAX	0.9537	MAX IV	MicroMAX

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	2.4	8.16	100	0.9799923	5.97707	396		10716

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	2.4	2.46			0.6700019

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	2.4	8.16	10674	555	96.887	0.15	0.147	0.1471	0.1993	0.1999	35.313

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]
0.137			0.137		-0.274

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.753
r_dihedral_angle_6_deg	15.339
r_scangle_it	10.782
r_lrange_it	10.621
r_dihedral_angle_2_deg	9.862
r_dihedral_angle_1_deg	8.687
r_scbond_it	8.279
r_mcangle_it	6.502
r_mcbond_it	5.096
r_angle_refined_deg	2.817
r_nbtor_refined	0.301
r_symmetry_nbd_refined	0.198
r_nbd_refined	0.196
r_chiral_restr	0.176
r_xyhbond_nbd_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.105
r_bond_refined_d	0.015
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1550
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms

Software

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