9G2J | pdb_00009g2j

Thaumatin structure determined using SoS chip at ID29 (serial crystallography)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FGT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7	293	0.8 M NA, K TARTRATE, 0.1 M NA HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.849	α = 90
b = 57.849	β = 90
c = 150.328	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		2023-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.073	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.69	38	100	0.067	15.1	4475		29237

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.69	1.8			0.73

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	1.69	37.904	29237	1412	98.934	0.158	0.1576	0.1691	0.1688	0.1755	28.84

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]
0.389			0.389		-0.777

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.535
r_dihedral_angle_3_deg	13.898
r_lrange_it	8.558
r_lrange_other	8.523
r_dihedral_angle_2_deg	8.124
r_scangle_other	7.439
r_scangle_it	7.438
r_dihedral_angle_1_deg	6.946
r_scbond_other	4.924
r_scbond_it	4.922
r_mcangle_other	3.388
r_mcangle_it	3.385
r_mcbond_it	2.499
r_mcbond_other	2.488
r_angle_refined_deg	1.751
r_angle_other_deg	0.64
r_xyhbond_nbd_refined	0.238
r_symmetry_nbd_refined	0.214
r_nbd_refined	0.21
r_nbd_other	0.21
r_symmetry_nbd_other	0.2
r_symmetry_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.194
r_symmetry_nbtor_other	0.095
r_chiral_restr	0.089
r_xyhbond_nbd_other	0.028
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
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	128
Heterogen Atoms	10

Software

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