9P14 | pdb_00009p14

Thaumatin Room-Temperature In-Situ, Grown On-Site

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.59 M di-ammonium tartrate

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.2	α = 90
b = 58.2	β = 90
c = 150.445	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	DECTRIS EIGER2 X 4M		2024-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.7749	Diamond	VMXi

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.78	54.2	99.9	0.163	0.183	0.078	0.997	7.9	8		25718

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.82			1.397	1.747	1.023	0.337		4.5

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	1.78	54.2	25638	1257	99.856	0.16	0.1587	0.1567	0.1898	0.1868	24.397

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]
0.506			0.506		-1.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.321
r_dihedral_angle_3_deg	12.893
r_dihedral_angle_2_deg	7.722
r_dihedral_angle_1_deg	7.455
r_lrange_it	7.109
r_lrange_other	7.075
r_scangle_it	6.259
r_scangle_other	6.259
r_scbond_other	4.222
r_scbond_it	4.219
r_mcangle_it	3.331
r_mcangle_other	3.33
r_mcbond_it	2.424
r_mcbond_other	2.409
r_angle_refined_deg	2.143
r_angle_other_deg	0.792
r_xyhbond_nbd_refined	0.506
r_symmetry_nbd_refined	0.43
r_nbd_refined	0.252
r_symmetry_nbd_other	0.205
r_nbtor_refined	0.192
r_nbd_other	0.164
r_chiral_restr	0.111
r_symmetry_xyhbond_nbd_refined	0.111
r_symmetry_nbtor_other	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1528
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
Coot	model building
xia2.multiplex	data reduction