Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Sequence details
RESIDUE NUMBERING IS BASED ON R.P.AMBLER ET AL. (BIOCHEM. J., V. 276, P. 269, 1991). THEREFORE, ...RESIDUE NUMBERING IS BASED ON R.P.AMBLER ET AL. (BIOCHEM. J., V. 276, P. 269, 1991). THEREFORE, THERE ARE NO RESIDUES NUMBERED 58, 84, 85, 239, AND 253.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: PEG 4000 28%, Sodium Citrate 0.1 M, pH 5.4, vapor diffusion, hanging drop, temperature 293K
Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 25, 2010
Radiation
Monochromator: A curved crystal silicon, with asymmetrical cuts. Asymmetry angle of 25.7, condensed mode. Range of energies of photons of X-rays 6 keV-12 keV (1A-2A) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.43 Å / Relative weight: 1
Reflection
Resolution: 1.729→55.045 Å / Num. all: 50182 / Num. obs: 50182 / % possible obs: 96.4 % / Redundancy: 3.7 % / Rsym value: 0.061 / Net I/σ(I): 13.9
Resolution: 1.729→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.027 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19264
2574
5.1 %
RANDOM
Rwork
0.16951
-
-
-
obs
0.17066
48058
96.89 %
-
all
-
50748
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 11.445 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.17 Å2
0 Å2
-0.5 Å2
2-
-
0.03 Å2
0 Å2
3-
-
-
0.14 Å2
Refinement step
Cycle: LAST / Resolution: 1.729→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3988
0
26
314
4328
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.02
4066
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.36
1.994
5498
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.626
5
510
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.331
25
188
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.352
15
742
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.923
15
30
X-RAY DIFFRACTION
r_chiral_restr
0.147
0.2
638
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
3046
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
0.809
1.5
2575
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.304
2
4141
X-RAY DIFFRACTION
r_scbond_it
2.324
3
1516
X-RAY DIFFRACTION
r_scangle_it
3.556
4.5
1379
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.729→1.774 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.272
209
-
Rwork
0.246
3331
-
obs
-
-
92.79 %
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
0.8271
0.031
0.1385
0.4967
-0.1375
0.4387
0.0406
-0.0249
0.0048
-0.0021
-0.0188
0.0006
0.0068
0.0102
-0.0218
0.0115
-0.0048
0.0053
0.0047
0.0003
0.0091
0.1429
25.9132
11.4623
2
0.6512
0.0228
-0.1428
0.3759
-0.1051
0.5276
0.0133
-0.0032
0.0019
-0.0044
-0.011
0.0143
0.0028
0.0047
-0.0023
0.0164
0
-0.012
0.0016
0.0011
0.0111
-4.9765
-5.5406
15.5708
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
31 - 291
2
X-RAY DIFFRACTION
1
A
300
3
X-RAY DIFFRACTION
2
B
31 - 291
4
X-RAY DIFFRACTION
2
B
300
+
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