3ZEJ | pdb_00003zej

Thaumatin structure determined at room temperature by in-situ diffraction in ChipX

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KWN	PDB ENTRY 1KWN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	6.5	293	THAUMATIN WAS CRYSTALLIZED AT 293 K BY COUNTER-DIFFUSION IN A CHIPX MICROFLUIDIC DEVICE. MICROFLUIDIC CHANNELS WERE FILLED WITH A 30 MG/ML THAUMATIN SOLUTION CONTAINING 0.3% BETA-OCTYL-GLUCOSIDE (M/V) TO FACILITATE SAMPLE LOADING BY CAPILLARITY. CRYSTALLANT RESERVOIRS WERE FILLED WITH 1.5 M SODIUM TARTRATE AND 0.1 M ADA PH 6.5.

Crystal Properties
Matthews coefficient	Solvent content
2.9	58.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.57	α = 90
b = 58.57	β = 90
c = 151.79	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	298	PIXEL	DECTRIS PILATUS 2M		2012-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA		SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.55	60	99.1	0.11	11.04	7		39090		-3	16.89

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.64	99.8		0.59	2.3	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1KWN	1.55	46.368	3.04	39050	1953	99.26	0.1627	0.1613	0.16	0.188	0.19	25.42

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.768
f_angle_d	1.069
f_chiral_restr	0.075
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1550
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	10

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.