7DKT | pdb_00007dkt

Crystal structure of TxGH116 E441A nucleophile mutant from Thermoanaerobacterium xylanolyticum with alpha-glucosyl fluoride

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5BVU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	288	0.14 M AMMONIUM SULFATE, 21% PEG 3350, 0.1 M MES, PH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.049	α = 90
b = 54.689	β = 90
c = 83.24	γ = 90

Symmetry
Space Group	P 21 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	RAYONIX MX300HE		2016-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.65	89	99.6	0.985	5.1	7.5		97660

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	99.1		0.83		7.5

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	5BVU	1.65	88.52	90318	4685	96.84	0.1616	0.1602	0.17	0.1873	0.2	RANDOM	16.882

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]
-0.23			0.35		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.475
r_dihedral_angle_4_deg	16.911
r_dihedral_angle_3_deg	11.981
r_dihedral_angle_1_deg	6.264
r_angle_refined_deg	1.344
r_angle_other_deg	0.917
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.475
r_dihedral_angle_4_deg	16.911
r_dihedral_angle_3_deg	11.981
r_dihedral_angle_1_deg	6.264
r_angle_refined_deg	1.344
r_angle_other_deg	0.917
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6217
Nucleic Acid Atoms
Solvent Atoms	652
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
HKL-2000	data scaling
MOLREP	phasing
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.