Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal grow
Temperature: 277 K / Method: microbatch technique under oil / pH: 8.5 Details: 0.085 M TRIS HCl (pH 8.5), 25.5% w/v PEG4000 15% glycerol, microbatch technique under oil, temperature 277K
Type: MAR CCD 165 mm / Detector: CCD / Date: 2008 Details: Slits: Variable vertical and horizontal slits. Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. ...Details: Slits: Variable vertical and horizontal slits. Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2.5 and 4.5 m. Distance from the monochromator to source is ~10.5 m.
Radiation
Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2. ...Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2.5 and 4.5 m. Distance from the monochromator to source is ~10.5 m. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9797 Å / Relative weight: 1
Reflection
Resolution: 1.55→30 Å / Num. obs: 57244 / % possible obs: 97.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 23.8
Reflection shell
Resolution: 1.55→1.61 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3603 / % possible all: 81.6
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
MAR345dtb
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
SOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.679 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOR STRUCTURE DETERMINATION, AUTHORS STATE THAT THE INITIAL MODEL IS SOLVED BY USING ANOMALOUS DATA ON A CRYSTAL DIFFERENT FROM WHAT WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FOR STRUCTURE DETERMINATION, AUTHORS STATE THAT THE INITIAL MODEL IS SOLVED BY USING ANOMALOUS DATA ON A CRYSTAL DIFFERENT FROM WHAT WAS DESCRIBED IN REMARK 200. THE FINAL STRUCTURE WAS REFINED BY USING THE INITIAL MODEL AND THE DATA DESCRIBED IN REMARK 3 AND REMARK 200.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22577
3060
5.1 %
RANDOM
Rwork
0.19355
-
-
-
obs
0.19518
57244
98.37 %
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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: 24.107 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.13 Å2
0 Å2
0 Å2
2-
-
0.86 Å2
0 Å2
3-
-
-
-0.73 Å2
Refinement step
Cycle: LAST / Resolution: 1.55→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2833
0
55
420
3308
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
2963
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.361
2.011
4027
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.019
5
372
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.099
22.24
125
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.167
15
466
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.175
15
29
X-RAY DIFFRACTION
r_chiral_restr
0.085
0.2
444
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2260
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.193
0.2
1443
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.304
0.2
2022
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.111
0.2
298
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
0.136
0.2
34
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.15
0.2
15
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
0.707
1.5
1885
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.078
2
2931
X-RAY DIFFRACTION
r_scbond_it
1.892
3
1216
X-RAY DIFFRACTION
r_scangle_it
2.976
4.5
1096
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.55→1.591 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.323
200
-
Rwork
0.303
3603
-
obs
-
3603
85 %
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
0.8496
-0.0706
-0.6183
1.1963
0.5419
2.0769
-0.0666
0.1336
-0.0974
0.0587
-0.0029
0.0297
0.3558
-0.0012
0.0695
-0.0403
-0.0098
0.0053
-0.0425
-0.0131
-0.0535
33.9392
50.0008
-1.8573
2
1.9553
0.4829
-0.0165
0.9861
-0.1021
2.9803
0.0439
-0.1721
0.0421
0.2696
-0.0383
0.1007
-0.0464
-0.2093
-0.0056
-0.0225
0.0107
0.0447
-0.0834
0.0082
-0.063
25.3191
61.1243
25.2918
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
3 - 178
3 - 178
2
X-RAY DIFFRACTION
2
A
A
187 - 372
187 - 372
+
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