2PE7

Thaumatin from Thaumatococcus Danielli in complex with tris-dipicolinate Europium

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.7 M Sodium Potassium Tatrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.55	α = 90
b = 57.55	β = 90
c = 149.4	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	100	CCD	MAR CCD 165 mm	Si(111)	2004-12-25	M	MAD
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	1.776211, 0.920134	ESRF	BM30A
2				ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.456	45.596	99.5	0.074	0.074	5.5	12.3		44812			11.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.53	96.7		0.39	0.39	1.1	7.7	6218

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1RQW	1.46	53.68	44636	2259	99.31	0.153	0.152	0.176	RANDOM	10.078

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]
0.06			0.06		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.729
r_dihedral_angle_4_deg	17.205
r_dihedral_angle_3_deg	12.83
r_dihedral_angle_1_deg	6.686
r_sphericity_free	4.884
r_angle_other_deg	3.975
r_scangle_it	3.064
r_scbond_it	2.192
r_mcangle_it	1.642
r_sphericity_bonded	1.439
r_angle_refined_deg	1.416
r_rigid_bond_restr	1.212
r_mcbond_it	1.11
r_mcbond_other	0.672
r_symmetry_vdw_other	0.28
r_symmetry_vdw_refined	0.231
r_nbd_other	0.23
r_nbd_refined	0.206
r_nbtor_refined	0.186
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.156
r_nbtor_other	0.118
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_other	0.009
r_gen_planes_refined	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1551
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	57

Software

Software
Software Name	Purpose
SCALA	data scaling
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BM30A	data collection
XDS	data reduction