4QDW | pdb_00004qdw

Joint X-ray and neutron structure of Streptomyces rubiginosus D-xylose isomerase in complex with two Ni2+ ions and linear L-arabinose

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.19	α = 90
b = 99.67	β = 90
c = 102.94	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++	OSMIC VARIMAX	2012-03-20	M	SINGLE WAVELENGTH
2	1	neutron	291	AREA DETECTOR	3He position sensitive detector		2011-08-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54
2	NUCLEAR REACTOR		2.422		D19

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	34.23	99.5	0.076						8.7	3.5		64130	2		10.1
2	1.8	71.6	81.5	0.12						10.5	2.7		36814	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.65		0.383						2.4	3.3
	1.8	1.9		0.49						1.5	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.8	20		2	36814	28443	1446		0.166	0.166	0.166		0.179		random	29

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_torsion_deg	17.8
x_angle_deg	0.9
x_torsion_impr_deg	0.84
x_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3054
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms	13

Software

Software
Software Name	Purpose
nCNS	refinement
d*TREK	data scaling
HKL-3000	data reduction
RETREAT	data reduction
HKL-3000	data scaling
RETREAT	data scaling
CNS	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.