Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES (pH 6.5), 2 mM MnCl2, 17% PEG 20000, vapor diffusion, hanging drop, temperature 298K
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Data collection
Diffraction source
Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
Detector
Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 2.2→59.88 Å / Num. obs: 12282 / % possible obs: 100 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.2-2.32
3.8
0.216
3.3
6819
1791
0.216
100
2.32-2.46
3.9
0.166
4.2
6500
1688
0.166
100
2.46-2.63
3.9
0.133
5.1
6066
1572
0.133
100
2.63-2.84
3.9
0.102
6.7
5732
1475
0.102
100
2.84-3.11
3.9
0.073
9.2
5318
1362
0.073
100
3.11-3.48
3.9
0.058
11.2
4862
1241
0.058
100
3.48-4.02
3.9
0.049
12.6
4282
1088
0.049
100
4.02-4.92
3.9
0.046
12.7
3633
924
0.046
100
4.92-6.96
3.9
0.047
12.9
2843
730
0.047
100
6.96-39.53
3.6
0.052
11
1494
411
0.052
99.7
-
Phasing
Phasing
Method: molecular replacement
Phasing MR
Model details: Phaser MODE: MR_AUTO
Highest resolution
Lowest resolution
Rotation
2.5 Å
39.53 Å
Translation
2.5 Å
39.53 Å
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Processing
Software
Name
Version
Classification
NB
MOSFLM
datareduction
SCALA
3.2.25
datascaling
PHASER
phasing
REFMAC
refinement
PDB_EXTRACT
3.005
dataextraction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→26.86 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.414 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.244
587
4.8 %
RANDOM
Rwork
0.191
-
-
-
obs
0.193
12276
100 %
-
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: 20.357 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→26.86 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2045
0
17
125
2187
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.022
2100
X-RAY DIFFRACTION
r_angle_refined_deg
1.065
1.974
2848
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.461
5
268
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.474
24.607
89
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.401
15
374
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.005
15
12
X-RAY DIFFRACTION
r_chiral_restr
0.065
0.2
325
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
1574
X-RAY DIFFRACTION
r_nbd_refined
0.175
0.2
1070
X-RAY DIFFRACTION
r_nbtor_refined
0.294
0.2
1462
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.129
0.2
167
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.168
0.2
39
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.163
0.2
11
X-RAY DIFFRACTION
r_mcbond_it
0.3
1.5
1364
X-RAY DIFFRACTION
r_mcangle_it
0.53
2
2149
X-RAY DIFFRACTION
r_scbond_it
0.753
3
830
X-RAY DIFFRACTION
r_scangle_it
1.249
4.5
699
LS refinement shell
Resolution: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.326
34
-
Rwork
0.234
878
-
all
-
912
-
obs
-
-
100 %
+
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