Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 10-20 mg/ml protein with 33 mm UDP and 66 mM MnCl2 with a precipitation solution containing 100 mM Tris.HCl, 1 M NaCl, 15% MPD and 5% PEG 4K., pH 8.0, VAPOR DIFFUSION, temperature 298K
Resolution: 1.81→1.87 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 1669 / Rsym value: 0.413 / % possible all: 85
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Processing
Software
Name
Version
Classification
HKL-3000
datacollection
SHELXS
phasing
REFMAC
5.5.0109
refinement
HKL-3000
datareduction
HKL-3000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: Brominated structure was solved using SAD at 2.0 A resolution and the cordinated are used as the stating model. Resolution: 1.81→36.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22059
2079
5 %
RANDOM
Rwork
0.18871
-
-
-
obs
0.19029
39114
97.83 %
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all
-
39114
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-0.01 Å2
0 Å2
0 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
0.01 Å2
Refinement step
Cycle: LAST / Resolution: 1.81→36.6 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1997
0
34
224
2255
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.023
0.021
2085
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.991
1.952
2826
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.738
5
240
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.158
23.364
110
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.172
15
356
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.884
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.163
0.2
298
X-RAY DIFFRACTION
r_gen_planes_refined
0.011
0.021
1596
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
1.212
1.5
1202
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.127
2
1949
X-RAY DIFFRACTION
r_scbond_it
3.405
3
883
X-RAY DIFFRACTION
r_scangle_it
5.105
4.5
877
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.81→1.857 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.329
134
-
Rwork
0.314
2347
-
obs
-
-
81.69 %
+
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