4LNC | pdb_00004lnc

Neutron structure of the cyclic glucose bound Xylose Isomerase E186Q mutant

NEUTRON DIFFRACTION - X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.7	295	Large crystals were grown in 1.5 ml Eppendorf tubes with 15% ammonium sulfate, 72 mg/ml D-xylose isomerase at ph 7.7, Batch method, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.97	α = 90
b = 99.52	β = 90
c = 102.92	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	IMAGE PLATE	EMBL PROTOTYPE LADI-I	Ni/Ti MULTILAYER	2000-06-04	L	LAUE
2	1	x-ray	293	IMAGE PLATE	MAR scanner 345 mm plate		2000-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	ILL BEAMLINE H142	3.6-5.0	ILL	H142
2	ROTATING ANODE		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	2.17	41.1	93	0.276	0.276					11.7	6.6		23649
2	1.83	25	83.2	0.173	0.173					4.3	2.4		35317

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	2.17	2.29		0.214	0.214					3.5	2.5
2	1.83	1.92		0.24	0.24					3.4	2.1

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		2.19	41.1				23628	2357	93.1		0.288	0.284		0.322
X-RAY DIFFRACTION		1.84	14.54		1.35		35159	3518	83.2		0.156	0.15	0.1557	0.209	0.1948		22.6826

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
f_dihedral_angle_d	19.247
f_angle_d	2.136
f_chiral_restr	0.156
f_bond_d	0.022
f_plane_restr	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3027
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	15

Software

Software
Software Name	Purpose
Quasi-Laue	data collection
PHENIX	refinement
LAUEGEN	data reduction
SCALA	data scaling
PHENIX	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.