3N8T | pdb_00003n8t

Native structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	100 mM sodium acetate (pH 5.5), 15% (w/v) PEG 8000, 10% (v/v) PEG 400 and 200 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.424	α = 90
b = 78.953	β = 90
c = 134.222	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD		2010-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.4586	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.4	68.1	99.3	0.09	12.6	4.2		29790			46.19

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.49	98.7		0.52	2.6	4.1	2906

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	PDB ENTRY 1UFA	2.4	68.05	28226	1510	99.2	0.18456	0.18148	0.1781	0.24181	0.2382	RANDOM	39.958

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]
-0.19			-0.03		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.099
r_dihedral_angle_4_deg	20.428
r_dihedral_angle_3_deg	17.439
r_dihedral_angle_1_deg	6.812
r_scangle_it	5.337
r_scbond_it	3.268
r_mcangle_it	2.118
r_angle_refined_deg	1.806
r_mcbond_it	1.113
r_chiral_restr	0.128
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4582
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	20

Software

Software
Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling