3CWH

D-xylose Isomerase in complex with linear product, per-deuterated xylulose

NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XIS	PDB entry 4XIS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	293	50MM TRIS-HCL, 38%(NH4)2SO4, 2MM MG2+ XI @ 125 MG/ML, PH=8.0, LIQUID DIFFUSION, T=293K; NATIVE CRYSTAL WERE SOAKED WITH 0.2M PER-DEUTERATED XYLOSE IN D2O BUFFERED IN 50MM TRIS-DCL, PH=7.6 (PD=8.0), 2MM MGCL2

Crystal Properties
Matthews coefficient	Solvent content
2.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.64	α = 90
b = 99.97	β = 90
c = 103.97	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	TIME-OF-FLIGHT MULTIWIRE HE3 NE		2004-09-01	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR				PCS

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	2.2	100	89.4	0.25	5.8	5.4		21892		1.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	81.3		0.38	2	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	PDB entry 4XIS	2.2	20	17072	876	86.3	0.237		0.288	RANDOM	20.7

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
s_angle_d	0.962
s_bond_d	0.007
s_similar_dist
s_from_restr_planes
s_zero_chiral_vol
s_non_zero_chiral_vol
s_anti_bump_dis_restr
s_rigid_bond_adp_cmpnt
s_similar_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3046
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	13

Software

Software
Software Name	Purpose
CNS	refinement
SHELXL-97	refinement
d*TREK	data reduction
LAUENORM	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.