Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: D2O
-
Experimental details
-
Experiment
Experiment
Method
Number of used crystals
NEUTRON DIFFRACTION
1
X-RAY DIFFRACTION
1
-
Sample preparation
Crystal
Density Matthews: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal grow
Temperature: 290 K / Method: batch / pH: 5.9 Details: 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 ...Details: 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
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
293
1
2
293
1
Diffraction source
Source
Beamline
Type
ID
Wavelength (Å)
NUCLEAR REACTOR
D19
1
2.422
ROTATING ANODE
RIGAKU FR-E DW
2
1.54
Detector
Type
ID
Detector
Date
He3-filled PSD
1
AREA DETECTOR
Jul 15, 2010
RIGAKU RAXIS IV++
2
IMAGE PLATE
Apr 5, 2010
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
GRAPHITE
SINGLEWAVELENGTH
M
neutron
1
2
SINGLEWAVELENGTH
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
2.422
1
2
1.54
1
Reflection
Entry-ID: 4DVO
Resolution (Å)
Num. obs
% possible obs (%)
Observed criterion σ(F)
Redundancy (%)
Rmerge(I) obs
Diffraction-ID
Net I/σ(I)
2-49.72
30585
93
2
4
0.154
1
7.6
1.55-29.9
68214
97.5
3.22
0.072
2
9.3
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Diffraction-ID
% possible all
2-2.1
2.4
0.408
1.8
1
90
1.55-1.61
2.66
0.347
2.6
2
93.5
-
Processing
Software
Name
Classification
CNS
refinement
nCNS
refinement
d*TREK
datareduction
d*TREK
datascaling
CNS
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.214
1501
5 %
RANDOM
Rwork
0.19
-
-
-
obs
0.19
30162
91.8 %
-
all
-
30585
-
-
Refinement step
Cycle: LAST / Resolution: 2→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3054
0
15
288
3357
Refine LS restraints
Refine-ID
Type
Dev ideal
NEUTRONDIFFRACTION
c_bond_d
0.006
NEUTRONDIFFRACTION
c_angle_deg
0.92
+
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