6T8E

Crystal structure of native xylose isomerase from Piromyces E2 grown in yeast, in complex with xylose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NH5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	14-17 % PEG3350, HEPES, pH 7

Crystal Properties
Matthews coefficient	Solvent content
2.3	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.454	α = 115.46
b = 79.267	β = 89.99
c = 91.878	γ = 117.07

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	MARRESEARCH		2018-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR-H	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.86	46.6	93.6	0.066	0.09	0.06	0.931	7.1	2.1		135735

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.89	79.1		0.38	0.518	0.35	0.286		1.9

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	FOURIER SYNTHESIS	THROUGHOUT	5NH5	1.86	46.6	128946	6788	93.61	0.1405	0.1386	0.1763	RANDOM	18.438

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]
1.1	0.55	-0.11	-0.28	-0.36	-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.68
r_dihedral_angle_4_deg	15.947
r_dihedral_angle_3_deg	14.367
r_dihedral_angle_1_deg	6.681
r_angle_refined_deg	1.55
r_angle_other_deg	1.443
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.68
r_dihedral_angle_4_deg	15.947
r_dihedral_angle_3_deg	14.367
r_dihedral_angle_1_deg	6.681
r_angle_refined_deg	1.55
r_angle_other_deg	1.443
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13876
Nucleic Acid Atoms
Solvent Atoms	1907
Heterogen Atoms	263

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

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 R01GM133198.