Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
THE CONFLICTS IN THE SEQUENCE IS BECAUSE THE AUTHORS USED THE GENEBANK SEQUENCE ACC55270.1 WHICH IS ...THE CONFLICTS IN THE SEQUENCE IS BECAUSE THE AUTHORS USED THE GENEBANK SEQUENCE ACC55270.1 WHICH IS A SLIGHTLY DIFFERENT STRAIN
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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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal grow
Temperature: 298 K / Method: microbatch under oil / pH: 7.2 Details: 20% PEG 3350, 0.2 M magnesium chloride at pH 7.2 , Microbatch under oil, temperature 298K
Type: MAR 225 / Detector: CCD / Date: Nov 25, 2008
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 3→50 Å / Num. all: 39424 / Num. obs: 36358 / % possible obs: 92.3 % / Redundancy: 4.9 % / Rsym value: 0.143 / Net I/σ(I): 34.2
Reflection shell
Resolution: 3→3.11 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 8.2 / Rsym value: 0.354 / % possible all: 75.6
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Processing
Software
Name
Version
Classification
HKL-2000
datacollection
PHASER
phasing
REFMAC
5.5.0044
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.888 / SU B: 42.467 / SU ML: 0.343 / Cross valid method: THROUGHOUT / ESU R Free: 0.49 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26047
1779
5.1 %
RANDOM
Rwork
0.20535
-
-
-
obs
0.2082
33421
87.96 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 40.805 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.05 Å2
-0 Å2
-0 Å2
2-
-
2.57 Å2
0 Å2
3-
-
-
-5.61 Å2
Refinement step
Cycle: LAST / Resolution: 3→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11341
0
236
68
11645
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.021
11827
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.085
1.961
15994
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.612
5
1439
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.628
24.359
585
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.316
15
1994
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.217
15
87
X-RAY DIFFRACTION
r_chiral_restr
0.074
0.2
1760
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
9010
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.825
3
7132
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.794
5
11468
X-RAY DIFFRACTION
r_scbond_it
3.354
8
4695
X-RAY DIFFRACTION
r_scangle_it
5.615
11
4526
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 3→3.078 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.361
86
-
Rwork
0.284
1632
-
obs
-
-
59.63 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.549
0.2586
-1.0567
0.7588
-0.9589
3.8918
0.0511
0.085
-0.0124
0.0747
0.0115
0.0234
-0.0729
-0.4161
-0.0626
0.0195
-0.0101
-0.0314
0.11
-0.0214
0.161
-30.5329
-10.7192
57.4793
2
0.3184
0.031
-0.9329
0.2463
-0.0602
6.264
0.0443
0.093
0.0355
-0.1211
-0.008
0.0742
-0.1376
-0.1211
-0.0363
0.0736
0.0123
-0.0279
0.0672
-0.0041
0.0299
-13.7278
-3.115
9.3261
3
0.5172
-0.1005
-0.6165
1.0933
1.0403
6.8032
0.0523
-0.0907
0.0353
0.2731
0.1356
-0.1374
0.4551
0.1277
-0.188
0.1015
0.0321
-0.0625
0.0705
-0.0521
0.1536
0.5406
-9.0435
66.482
4
1.0748
0.0209
-2.1258
0.2187
-0.0423
7.6188
0.0054
0.1317
-0.1194
-0.0586
-0.0093
-0.0813
0.3192
0.4508
0.0039
0.0477
0.0716
-0.0047
0.1671
-0.0509
0.0879
5.9637
-8.8625
15.1169
5
1.1038
-0.1365
-1.5674
0.5979
0.4646
3.9804
0.022
-0.0278
0.1315
0.0227
0.1111
0.0565
-0.1839
0.0687
-0.1331
0.0221
0.0071
-0.0155
0.021
0.0058
0.1206
-16.5368
18.0857
62.4966
6
0.6839
0.0503
-1.7894
0.1854
-0.4263
8.305
-0.027
-0.0078
0.0256
-0.1069
-0.0527
-0.075
-0.3225
0.4314
0.0797
0.1787
-0.0508
0.0502
0.0714
0.0109
0.0401
0.3747
11.7773
14.2289
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
-10 - 9999
2
X-RAY DIFFRACTION
2
B
-10 - 9999
3
X-RAY DIFFRACTION
3
C
-10 - 9999
4
X-RAY DIFFRACTION
4
D
-10 - 9999
5
X-RAY DIFFRACTION
5
E
-10 - 9999
6
X-RAY DIFFRACTION
6
F
-10 - 9999
+
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