5KW0 | pdb_00005kw0

T. danielli thaumatin at 100K, Data set 5

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, SITTING DROP	7.3	291	CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (0.9 M SODIUM/POTASSIUM TARTRATE, 0.2 M AMMONIUM SULFATE, 15% GLYCEROL, 25% PEG 8000, 100 MM HEPES PH 7.3) AND PROTEIN (35 MG/ML) IN THE SITTING DROP FORMAT.

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.814	α = 90
b = 57.814	β = 90
c = 151.2	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	MARMOSAIC 325 mm CCD		2014-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1.21549	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (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	1.593	31.749	99	0.059	0.068	0.033	11.1	4.1	34950	34950

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.593	1.68	94.5		3.129	3.129	3.72	1.962	0.2	3.3	4771

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RQW	1.594	31.749	30376	1610	90.87	0.1749	0.173	0.1864	0.2117	0.2244	RANDOM	34.284

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]
0.87			0.87		-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.14
r_dihedral_angle_4_deg	19.495
r_dihedral_angle_3_deg	16.568
r_dihedral_angle_1_deg	9.392
r_mcangle_it	3.956
r_mcbond_it	2.884
r_mcbond_other	2.756
r_angle_refined_deg	2.012
r_angle_other_deg	1.071
r_chiral_restr	0.128
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1551
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction