7DKU

Crystal structure of TxGH116 E441A nucleophile mutant from Thermoanaerobacterium xylanolyticum with cellobiose

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	0.16 M AMMONIUM SULFATE, 22% PEG 3000, 0.1 M MES, PH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.259	α = 90
b = 54.459	β = 90
c = 83.154	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	ADSC QUANTUM 315r		2018-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0	NSRRC	BL13B1

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	1.6	89	98.2	0.999	50.9	6.7		105220

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	1.6	1.66	91		0.973

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	5BVU	1.6	88.63	99857	5170	98.14	0.1568	0.1556	0.1797	RANDOM	14.986

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]
-0.05			0.01		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.717
r_dihedral_angle_4_deg	18.724
r_dihedral_angle_3_deg	11.514
r_dihedral_angle_1_deg	6.224
r_angle_refined_deg	1.314
r_angle_other_deg	0.914
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.717
r_dihedral_angle_4_deg	18.724
r_dihedral_angle_3_deg	11.514
r_dihedral_angle_1_deg	6.224
r_angle_refined_deg	1.314
r_angle_other_deg	0.914
r_chiral_restr	0.079
r_bond_refined_d	0.007
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	716
Heterogen Atoms	108

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.