3QZA

Joint neutron and X-ray structure of apo-D-Xylose Isomerase at pH=5.9

NEUTRON DIFFRACTION - X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	5.9	280	crystals grew with ammonium sulfate as a precipitant at pH of 5.9, batch crystallization, temperature 280K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.908	α = 90
b = 99.503	β = 90
c = 102.971	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	position sensitive He3		2010-09-15	L	TOF LAUE
2	1	x-ray	293	IMAGE PLATE	RIGAKU RAXIS IV++		2010-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	LANSCE BEAMLINE PCS	0.6-7.0	LANSCE	PCS
2	ROTATING ANODE	RIGAKU FR-E+ DW	1.5418

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	28.46	86.9	0.225						4.5	3	28290	28290	2.2	1.5
2	1.7	29.86	99.2	0.077						8.6	3.222	53087	53087

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	2.11		0.385	0.385					1.3	1.7
2	1.7	1.76		0.315	0.315					2.6	2.88

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	R-Free	R-Free Selection Details	Mean Isotropic B
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2	20		2.2	28290	26760	1347	81.4		0.254	0.254	0.28	RANDOM
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.7	20		2.5		49805	2507	93.6		0.254	0.195	0.211	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
x_dihedral_angle_d	17.9
x_dihedral_angle_d	17.9
x_angle_deg	1
x_angle_deg	1
x_improper_angle_d	0.82
x_improper_angle_d	0.82
x_bond_d	0.007
x_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3054
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms

Software

Software
Software Name	Purpose
nCNS	refinement
d*TREK	data scaling
d*TREK	data reduction
LAUENORM	data reduction
LAUENORM	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.