glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function
Type: MAR CCD 165 mm / Detector: CCD / Date: May 22, 2004
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.98 Å / Relative weight: 1
Reflection
Resolution: 1.66→50 Å / Num. obs: 35478 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 13.75 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.2
Reflection shell
Resolution: 1.66→1.72 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 13.23 / Num. unique all: 3469 / % possible all: 98.8
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
SOLVE
phasing
PHENIX
(phenix.refine: 1.6.4_486)
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.66→35.654 Å / FOM work R set: 0.9192 / SU ML: 0.14 / σ(F): 1.4 / Phase error: 14.43 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1664
1777
5.01 %
RANDOM
Rwork
0.1455
-
-
-
obs
0.1466
35455
99.41 %
-
all
-
35665
-
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.698 Å2 / ksol: 0.398 e/Å3
Displacement parameters
Biso mean: 15.1909 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.5846 Å2
0 Å2
0 Å2
2-
-
0.5846 Å2
-0 Å2
3-
-
-
-1.1693 Å2
Refine analyze
Luzzati coordinate error obs: 0.129 Å
Refinement step
Cycle: LAST / Resolution: 1.66→35.654 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1876
0
44
325
2245
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
2095
X-RAY DIFFRACTION
f_angle_d
1.307
2877
X-RAY DIFFRACTION
f_dihedral_angle_d
13.466
732
X-RAY DIFFRACTION
f_chiral_restr
0.102
274
X-RAY DIFFRACTION
f_plane_restr
0.009
383
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.66-1.7049
0.1848
140
0.1548
2546
X-RAY DIFFRACTION
98
1.7049-1.755
0.1416
114
0.1331
2581
X-RAY DIFFRACTION
100
1.755-1.8117
0.1866
144
0.1319
2581
X-RAY DIFFRACTION
100
1.8117-1.8764
0.1703
131
0.1318
2613
X-RAY DIFFRACTION
100
1.8764-1.9516
0.1858
133
0.1332
2576
X-RAY DIFFRACTION
100
1.9516-2.0404
0.17
152
0.1355
2587
X-RAY DIFFRACTION
100
2.0404-2.1479
0.1419
136
0.1371
2615
X-RAY DIFFRACTION
100
2.1479-2.2825
0.1709
123
0.1417
2597
X-RAY DIFFRACTION
100
2.2825-2.4587
0.1834
139
0.1501
2636
X-RAY DIFFRACTION
100
2.4587-2.706
0.1776
139
0.1534
2578
X-RAY DIFFRACTION
100
2.706-3.0974
0.1642
150
0.1465
2617
X-RAY DIFFRACTION
100
3.0974-3.9016
0.1323
141
0.1354
2614
X-RAY DIFFRACTION
100
3.9016-35.6627
0.189
135
0.171
2537
X-RAY DIFFRACTION
95
+
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