4QEE | pdb_00004qee

Room temperature X-ray structure of D-xylose isomerase in complex with two Ni2+ ions and L-ribose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch	7.7	291	30% ammonium sulfate, 0.1M HEPES pH 7.7, batch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.958	α = 90
b = 99.613	β = 90
c = 103.035	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	291	IMAGE PLATE	RIGAKU RAXIS IV++		2013-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	40	90.4			62669	56676	4	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FREE R	1.6	20	61997	56676	3102		0.1546	0.1472	0.1526	0.15	0.1912	0.18	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
4		3309.5

RMS Deviations
Key	Refinement Restraint Deviation
s_non_zero_chiral_vol	0.081
s_similar_adp_cmpnt	0.067
s_zero_chiral_vol	0.058
s_angle_d	0.027
s_anti_bump_dis_restr	0.025
s_from_restr_planes	0.0232
s_bond_d	0.011
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3053
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms	12

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
SHELXL-97	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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.