#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)
-
Assembly
Deposited unit
H: Motavizumab Fab heavy chain L: Motavizumab Fab light chain S: RSV_1Isea designed scaffold A: Motavizumab Fab heavy chain B: Motavizumab Fab light chain C: RSV_1Isea designed scaffold hetero molecules
Resolution: 2.7→2.75 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 6.8 / % possible all: 100
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
PHASER
phasing
REFMAC
5.7.0029
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→45.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 26.628 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24926
1867
5 %
RANDOM
Rwork
0.19134
-
-
-
obs
0.19424
35615
99.32 %
-
all
-
37548
-
-
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: 74.54 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.95 Å2
0 Å2
0 Å2
2-
-
2.04 Å2
0 Å2
3-
-
-
1.92 Å2
Refine analyze
Luzzati coordinate error obs: 0.752 Å
Refinement step
Cycle: LAST / Resolution: 2.71→45.84 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7806
0
12
98
7916
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.02
8002
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
7374
X-RAY DIFFRACTION
r_angle_refined_deg
1.228
1.953
10890
X-RAY DIFFRACTION
r_angle_other_deg
0.728
3.002
16988
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.655
5
1033
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.547
24.492
305
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.255
15
1252
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.996
15
30
X-RAY DIFFRACTION
r_chiral_restr
0.067
0.2
1255
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
9072
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1758
LS refinement shell
Resolution: 2.71→2.78 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.325
124
-
Rwork
0.238
2465
-
obs
-
-
94.18 %
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
4.8313
0.575
0.1348
2.2652
-1.5583
4.1968
-0.3764
1.1721
0.1891
-0.5636
0.131
0.3265
-0.1252
0.5131
0.2453
0.2381
-0.1093
-0.1746
0.6984
0.0184
0.1447
31.631
50.927
-4.684
2
5.4301
1.7753
0.3142
3.4126
-0.7162
3.3783
-0.3063
-0.078
0.6321
0.1451
0.0915
-0.0762
-0.5153
0.7211
0.2148
0.1072
-0.041
-0.0893
0.5414
-0.0839
0.1305
53.85
58.153
19.699
3
15.2346
-11.715
2.0054
13.487
-3.007
0.7871
1.2252
1.405
1.0328
-0.2929
-0.9447
0.561
-0.2372
0.2961
-0.2805
1.3014
-0.1108
-0.0969
1.301
0.1181
0.6256
2.519
66.731
-17.976
4
3.0191
-0.5795
-0.5351
1.8608
1.2291
2.6859
-0.0059
-0.1083
-0.0141
0.4176
0.0883
-0.1677
0.179
0.0673
-0.0823
0.117
-0.0186
-0.0661
0.1492
0.0623
0.0616
-18.174
50.927
6.032
5
1.7733
-1.3199
-1.6618
3.3617
1.7062
5.7385
0.0314
0.3845
0.1139
-0.3836
-0.1413
0.7058
-0.5608
-0.6049
0.1099
0.1416
-0.0594
-0.1329
0.3011
0.0946
0.2751
-44
65.365
-10.769
6
11.9679
6.8242
0.1875
11.4467
2.9399
4.3033
0.5782
-0.8816
0.4936
1.2453
0.1719
-1.2762
-0.2074
0.8055
-0.7501
0.3859
0.031
-0.3107
0.5515
-0.1954
0.6052
11.002
58.253
19.087
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 119
2
X-RAY DIFFRACTION
1
B
1 - 106
3
X-RAY DIFFRACTION
2
A
120 - 213
4
X-RAY DIFFRACTION
2
B
107 - 210
5
X-RAY DIFFRACTION
3
C
8 - 110
6
X-RAY DIFFRACTION
4
H
1 - 122
7
X-RAY DIFFRACTION
4
L
1 - 107
8
X-RAY DIFFRACTION
5
H
123 - 213
9
X-RAY DIFFRACTION
5
L
108 - 210
10
X-RAY DIFFRACTION
6
S
4 - 107
+
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