Experiment: 4DVO

Room-temperature joint X-ray/neutron structure of D-xylose isomerase in complex with 2Ni2+ and per-deuterated D-sorbitol at pH 5.9

NEUTRON DIFFRACTION - X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch	5.9	290	apo-Xylose isomerase crystals were grown with AmSO4 as precipitant and 0.1 M MES at pH 5.9; they then were injected with Ni2+ salt up to the concentration of 5mM and D-sorbitol up to the concentration of 300mM, batch, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.061	α = 90
b = 99.428	β = 90
c = 102.798	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	neutron	293	AREA DETECTOR	He3-filled PSD		2010-07-15	M	SINGLE WAVELENGTH
2	1	x-ray	293	IMAGE PLATE	RIGAKU RAXIS IV++		2010-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR		2.422		D19
2	ROTATING ANODE	RIGAKU FR-E DW	1.54

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	2	49.72	93	0.154						7.6	4		30585	2
2	1.55	29.9	97.5	0.072						9.3	3.22		68214

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	2	2.1		0.408						1.8	2.4
2	1.55	1.61		0.347						2.6	2.66

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	2	20		2	30585	30162	1501	91.8		0.19	0.19		0.214		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]

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	0.92
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3054
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	15

Software

Software
Software Name	Purpose
CNS	refinement
nCNS	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing