Mass: 47030.043 Da / Num. of mol.: 2 / Fragment: unp residues 23-128; unp residues 54-358 / Mutation: M29W, H124I, L51R, I135L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: cybC, OPRK1, OPRK / Production host: unidentified baculovirus / References: UniProt: P0ABE7, UniProt: P41145
#2: Antibody
Nanobody
Mass: 14913.330 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Lama glama (llama)
Resolution: 3.1→46.94 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.832 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.834 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.714 / SU Rfree Blow DPI: 0.374 / SU Rfree Cruickshank DPI: 0.391 Details: THERE ARE SOME UNKNOWN DENSITIES LOCATED ABOVE THE LIGAND BINDING SITE AND NEAR THE TRP222 ON BOTH A AND B CHAINS. THEY HAVE NOT BEEN MODELLED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.275
1505
4.97 %
RANDOM
Rwork
0.254
-
-
-
obs
0.255
30255
93.5 %
-
Displacement parameters
Biso mean: 85.74 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-29.6548 Å2
0 Å2
-3.2357 Å2
2-
-
21.5032 Å2
0 Å2
3-
-
-
8.1516 Å2
Refine analyze
Luzzati coordinate error obs: 0.6 Å
Refinement step
Cycle: 1 / Resolution: 3.1→46.94 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6006
0
136
0
6142
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
6307
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.95
8661
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2728
SINUSOIDAL
15
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
81
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
931
HARMONIC
5
X-RAY DIFFRACTION
t_it
6307
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.54
X-RAY DIFFRACTION
t_other_torsion
1.57
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
901
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
7781
SEMIHARMONIC
4
LS refinement shell
Resolution: 3.1→3.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
Rfactor
Num. reflection
% reflection
Rfree
0.283
138
5.1 %
Rwork
0.245
2570
-
all
0.247
2708
-
obs
-
-
85.61 %
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
0.6808
-0.1949
-0.3377
2.5682
0.9759
1.6936
0.0929
-0.1566
-0.0532
-0.1717
0.0023
0.0208
0.0122
-0.0852
-0.0952
0.0608
-0.0397
-0.0984
-0.1567
0.0077
-0.1908
61.2141
-21.9866
5.1559
2
0.7626
-0.3708
0.1139
2.1248
0.6449
1.0044
0.0418
0.1213
-0.0641
0.286
-0.0921
-0.029
-0.0033
-0.1052
0.0503
0.1822
-0.0208
-0.0436
-0.1697
0.0206
-0.2378
56.7465
13.9345
-5.7761
3
4.8117
1.6414
1.1
2.934
1.0974
4.7865
-0.0681
-0.0728
0.3412
-0.0963
0.0442
0.1442
-0.2113
-0.0197
0.0239
0.0541
0.06
-0.0929
-0.1786
0.0343
-0.2251
49.9534
3.0159
-40.5571
4
2.7839
-2.0803
-2.0908
3.4103
1.8807
6.155
-0.0191
0.0475
-0.2738
0.2529
0.1427
0.0658
-0.0334
-0.0208
-0.1237
0.1137
-0.0409
-0.0531
-0.2278
0.0609
-0.2442
53.6609
-9.7035
39.7407
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ A|51 - A|339 }
2
X-RAY DIFFRACTION
2
{ B|54 - B|334 }
3
X-RAY DIFFRACTION
3
{ C|4 - C|129 }
4
X-RAY DIFFRACTION
4
{ D|4 - D|129 }
+
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