3N98

Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose and additives

X-RAY DIFFRACTION

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, 200 mM sodium chloride, 1% (v/v) dioxane and 5% (v/v) glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.674	α = 90
b = 79.02	β = 90
c = 134.088	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	1.87	68.08	95.4	0.104	24	10.8		59969			24.6

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)
	1.87	1.94	84.3		0.481	2.2	4.8	5216

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UFA	1.87	68.08	56854	3024	95.42	0.16107	0.15929	0.1959	RANDOM	25.03

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]
0.74			0.05		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.516
r_dihedral_angle_4_deg	18.264
r_dihedral_angle_3_deg	15.61
r_dihedral_angle_1_deg	6.087
r_scangle_it	5.982
r_scbond_it	3.879
r_mcangle_it	2.548
r_angle_refined_deg	2.21
r_mcbond_it	1.554
r_chiral_restr	0.232

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.516
r_dihedral_angle_4_deg	18.264
r_dihedral_angle_3_deg	15.61
r_dihedral_angle_1_deg	6.087
r_scangle_it	5.982
r_scbond_it	3.879
r_mcangle_it	2.548
r_angle_refined_deg	2.21
r_mcbond_it	1.554
r_chiral_restr	0.232
r_bond_refined_d	0.031
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4582
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	86

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.