Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
N
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 25066
-
Sample preparation
Crystal
Density Matthews: 5.11 Å3/Da / Density % sol: 75.93 %
Crystal grow
Temperature: 295 K / Method: batch mode / pH: 5.5 Details: NendoU protein 75 mg/ml (20 mM HEPES pH 7.5, 150mM NaCl, 1mM TCEP) is added to the precipitant solution (100mM Na Citrate pH 5.5, 20% PEG 1000, 20% 2-Methyl-2,4-pentanediol (MPD)) in a 1:7 ...Details: NendoU protein 75 mg/ml (20 mM HEPES pH 7.5, 150mM NaCl, 1mM TCEP) is added to the precipitant solution (100mM Na Citrate pH 5.5, 20% PEG 1000, 20% 2-Methyl-2,4-pentanediol (MPD)) in a 1:7 protein:precipitant ratio with agitation at 295K overnight.
-
Data collection
Diffraction
Mean temperature: 295 K / Serial crystal experiment: Y
Diffraction source
Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.277 Å
Resolution: 2.6→33.67 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.183 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20877
2503
5.2 %
RANDOM
Rwork
0.19137
-
-
-
obs
0.19229
45981
99.9 %
-
Solvent computation
Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parameters
Biso mean: 47.684 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-8.54 Å2
-0 Å2
-0 Å2
2-
-
-8.54 Å2
-0 Å2
3-
-
-
17.07 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→33.67 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5504
0
26
16
5546
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.019
5644
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
5243
X-RAY DIFFRACTION
r_angle_refined_deg
1.034
1.884
7657
X-RAY DIFFRACTION
r_angle_other_deg
0.909
2.934
12202
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.347
5
694
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.26
25.331
257
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.785
15
980
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.657
15
18
X-RAY DIFFRACTION
r_chiral_restr
0.06
0.2
873
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
6238
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1100
X-RAY DIFFRACTION
r_mcbond_it
0.458
4.021
2782
X-RAY DIFFRACTION
r_mcbond_other
0.458
4.02
2781
X-RAY DIFFRACTION
r_mcangle_it
0.829
6.028
3474
X-RAY DIFFRACTION
r_mcangle_other
0.829
6.029
3475
X-RAY DIFFRACTION
r_scbond_it
0.267
4.079
2862
X-RAY DIFFRACTION
r_scbond_other
0.266
4.077
2859
X-RAY DIFFRACTION
r_scangle_other
0.502
6.098
4184
X-RAY DIFFRACTION
r_long_range_B_refined
1.278
44.867
5629
X-RAY DIFFRACTION
r_long_range_B_other
1.278
44.872
5630
LS refinement shell
Resolution: 2.6→2.667 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.299
191
-
Rwork
0.283
3372
-
obs
-
-
99.78 %
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
0.5353
-0.084
-0.0367
0.5634
-0.1235
0.4455
0.0107
0.1157
0.0921
-0.109
-0.012
-0.0003
-0.0475
0.0079
0.0013
0.1485
-0.0039
-0.0326
0.1555
0.0032
0.0741
-13.883
-71.205
4.985
2
0.6337
0.185
0.2785
0.5123
0.0801
0.4829
-0.0163
-0.0946
-0.0394
0.0593
0.003
-0.0554
0.0322
0.0007
0.0133
0.1264
0.0063
0.0151
0.1299
0.022
0.0626
-59.41
-58.456
-5.083
+
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