6T8F

Crystal structure of mutant xylose isomerase (V270A/A273G) from Piromyces E2 grown in yeast, in complex with xylose

X-RAY DIFFRACTION

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.598	α = 115.46
b = 79.372	β = 89.98
c = 91.982	γ = 117.13

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		2018-08-29	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	2	46.6	95.3	0.083	0.111	0.074	0.992	5.3	2.2		111563

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	2	2.03	92.1		0.355	0.479	0.32	0.772		2.2

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	2	46.6	105998	5562	95.26	0.1507	0.1489	0.1849	RANDOM	22.255

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]
1.83	1.06	0.14	-0.1	-0.38	-1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.716
r_dihedral_angle_4_deg	18.376
r_dihedral_angle_3_deg	14.201
r_dihedral_angle_1_deg	6.547
r_angle_refined_deg	1.549
r_angle_other_deg	1.432
r_chiral_restr	0.083
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	35.716
r_dihedral_angle_4_deg	18.376
r_dihedral_angle_3_deg	14.201
r_dihedral_angle_1_deg	6.547
r_angle_refined_deg	1.549
r_angle_other_deg	1.432
r_chiral_restr	0.083
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	13864
Nucleic Acid Atoms
Solvent Atoms	1724
Heterogen Atoms	218

Software

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