5KVW | pdb_00005kvw

T. danielli thaumatin at 100K, Data set 1

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
2.8	56.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.469	α = 90
b = 57.469	β = 90
c = 150.933	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	1.59	31.613	99	0.044	0.05	0.024	15.1	4.1	34655	34655

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	1.59	1.68	95.3		0.728	0.728	0.863	0.452	1.1	3.4	4767

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	1.59	31.61	32840	1733	98.78	0.164	0.1622	0.1693	0.1956	0.1974	RANDOM	26.895

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]
0.95			0.95		-1.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.603
r_dihedral_angle_4_deg	21.074
r_dihedral_angle_3_deg	14.995
r_dihedral_angle_1_deg	8.75
r_mcangle_it	3.206
r_mcbond_it	2.266
r_mcbond_other	2.254
r_angle_refined_deg	2.15
r_angle_other_deg	1.155
r_chiral_restr	0.124
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1551
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	28

Software

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