Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 3 M Na malonate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Monochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9793 Å / Relative weight: 1
Reflection
Resolution: 2.19→48.6 Å / Num. all: 48479 / Num. obs: 45445 / % possible obs: 93.5 %
Reflection shell
Resolution: 2.19→2.25 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2836 / Rsym value: 0.631 / % possible all: 89.3
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Processing
Software
Name
Version
Classification
ADSC
Quantum
datacollection
PHASER
phasing
REFMAC
5.5.0109
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→48.6 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.181 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2242
2295
5.1 %
RANDOM
Rwork
0.19206
-
-
-
obs
0.19369
43149
93.74 %
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all
-
45445
-
-
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: 44.913 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.6 Å2
0 Å2
-0 Å2
2-
-
0.96 Å2
0 Å2
3-
-
-
-0.37 Å2
Refinement step
Cycle: LAST / Resolution: 2.19→48.6 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4751
0
0
215
4966
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
4858
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.572
1.957
6599
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.621
5
613
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.311
25.101
198
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.174
15
831
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.326
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.105
0.2
747
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
3623
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
0.897
1.5
3065
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.73
2
4970
X-RAY DIFFRACTION
r_scbond_it
2.582
3
1793
X-RAY DIFFRACTION
r_scangle_it
4.268
4.5
1629
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.19→2.252 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.28
152
-
Rwork
0.259
2836
-
obs
-
-
85.35 %
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
1.7315
-0.0186
1.3527
0.2476
0.0358
1.7138
0.0243
-0.0949
0.0709
0.1214
-0.0726
0.0081
0.0215
-0.1703
0.0483
0.1293
-0.0236
-0.0006
0.2684
0.0082
0.0872
3.758
15.592
57.388
2
2.116
-0.5813
1.3705
0.3255
-0.6698
1.5394
0.2106
0.4124
-0.1605
0.0191
-0.1495
0.0115
0.1109
0.298
-0.061
0.1553
0.0304
-0.0305
0.3242
-0.0174
0.0974
13.251
5.862
46.16
3
2.642
1.2648
-0.7443
1.1762
0.1488
2.7514
-0.0456
0.6024
-0.0487
-0.1448
0.0767
0.1012
0.1514
-0.0872
-0.0311
0.0759
0.0514
-0.047
0.731
-0.0352
0.043
-12.896
9.347
12.078
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
L
-10 - 9999
2
X-RAY DIFFRACTION
2
H
-10 - 9999
3
X-RAY DIFFRACTION
3
A
-10 - 9999
+
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