3KBW | pdb_00003kbw

Room temperature X-ray mixed-metal structure of D-Xylose Isomerase in complex with Ni(2+) and Mg(2+) co-factors

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch	7.7	290	40mg/ml protein, 2mM NiCl2, 2mM MgCl2, 30% (v/v) ammonium sulfate (sat.), pH 7.7, batch, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.972	α = 90
b = 99.701	β = 90
c = 102.855	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	293	IMAGE PLATE	RIGAKU RAXIS IV++		2008-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE		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	10	80			62867	50014	4	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.65	95

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	AB INITIO	FREE R	1.6	10	62867	3131	98.9	0.1216	0.1192		0.12	0.1665	0.17	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
3		3338

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.114
s_non_zero_chiral_vol	0.063
s_similar_adp_cmpnt	0.061
s_zero_chiral_vol	0.047
s_angle_d	0.029
s_from_restr_planes	0.0232
s_anti_bump_dis_restr	0.015
s_bond_d	0.012
s_rigid_bond_adp_cmpnt	0.005
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3053
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	2

Software

Software
Software Name	Purpose
CrystalClear	data collection
SHELX	model building
SHELXL-97	refinement
CrystalClear	data reduction
CrystalClear	data scaling
SHELX	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 R01GM157729.