Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal grow
Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 1ul of protein at 20mg/ml mixed with 1ul of mother liquor, plus 0.2ul of a seed stock made from a previous crystallization drop. Crystallization condition is 0.1M Citric Acid pH 3.5, 25% PEG 3350. Temp details: Temperature Controlled Crystal Incubator
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Data collection
Diffraction
Mean temperature: 80 K / Ambient temp details: Liquid Nitrogen Cryo Stream
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.75141 Å
Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.75141 Å / Relative weight: 1
Reflection
Resolution: 1→44.333 Å / Num. obs: 181340 / % possible obs: 100 % / Redundancy: 4.5 % / Biso Wilson estimate: 8.14 Å2 / Rmerge(I) obs: 0.058 / Net I/av σ(I): 21 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
CC1/2
Diffraction-ID
% possible all
1-1.02
3.7
0.973
0.89
0.557
1
99.9
1.02-1.04
4.1
0.793
1.22
0.681
1
100
1.04-1.06
4.4
0.682
1.53
0.754
1
100
1.06-1.08
4.5
0.528
2
0.839
1
100
1.08-1.1
4.5
0.425
2.63
0.882
1
100
1.1-1.13
4.5
0.337
3.44
0.929
1
100
1.13-1.15
4.5
0.284
4.06
0.948
1
100
1.15-1.19
4.5
0.253
4.8
0.955
1
100
1.19-1.22
4.5
0.227
5.2
0.961
1
100
1.22-1.26
4.5
0.202
6.29
0.968
1
100
1.26-1.3
4.6
0.18
6.71
0.976
1
100
1.3-1.36
4.6
0.154
8.15
0.981
1
100
1.36-1.42
4.6
0.129
9.69
0.986
1
100
1.42-1.49
4.6
0.106
12.3
0.99
1
100
1.49-1.59
4.6
0.089
16.46
0.993
1
100
1.59-1.71
4.6
0.078
20.07
0.993
1
100
1.71-1.88
4.6
0.064
26.35
0.995
1
100
1.88-2.15
4.5
0.045
36.77
0.997
1
100
2.15-2.71
4.6
0.034
41.58
0.998
1
100
2.71-50
4.7
0.023
54.12
0.999
1
100
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Phasing
Phasing
Method: molecular replacement
Phasing MR
Highest resolution
Lowest resolution
Rotation
1.04 Å
19.29 Å
Translation
1.04 Å
19.29 Å
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Processing
Software
Name
Version
Classification
HKL-2000
v708c
datareduction
HKL-2000
v708c
datascaling
PHASER
2.7.0
phasing
Coot
0.8.2
modelbuilding
PHENIX
dev_2841
refinement
PDB_EXTRACT
3.2
dataextraction
HKL
datareduction
HKL
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: Fen49 Computational Design, with residues 63, 85-95 and 116-122 removed Resolution: 1→44.333 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 10.88 Details: Interative rounds of model building in Coot and refinement in Phenix. Refinement in real and reciprocal space, all-atom (except H) anisotropic ADP refinement, occupancy refinement. ...Details: Interative rounds of model building in Coot and refinement in Phenix. Refinement in real and reciprocal space, all-atom (except H) anisotropic ADP refinement, occupancy refinement. Optimization of X-ray to stereochemistry and X-ray to ADP weights. Automatic addition of hydrogens to the model, and automatic correction of N/Q/H errors. Several rounds of updating waters during refinement. Manual inspection and correction of waters before the final round of refinement.
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