Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein
3C-likeproteinasensp5 / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase
Mass: 33841.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli (E. coli) References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Protein/peptide
Macrocyclicpeptideinhibitor
Mass: 1562.817 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
-
Details
Has ligand of interest
Y
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.34 Å3/Da / Density % sol: 47.56 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Mpro was thawed and diluted to 6 mg/ml using 20 mM Hepes pH 7.5, 50 mM NaCl. GM4 was diluted into the protein solution to a final concentration of 10 mM and allowed to incubate for two hours ...Details: Mpro was thawed and diluted to 6 mg/ml using 20 mM Hepes pH 7.5, 50 mM NaCl. GM4 was diluted into the protein solution to a final concentration of 10 mM and allowed to incubate for two hours at room temperature prior to dispensing plates. The drop composition was 0.15 ul protein ligand solution, 0.3 ul 11% (v/v) PEG 4K, 0.1 M MES pH 6.5, and 0.05 ul Mpro crystal seed stock. The Mpro crystal seed stock was prepared by crushing Mpro crystals with a pipette tip, suspending them in 30% PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5, and vortexing for 60 s with approximately 10 glass beads (1.0 mm diameter, BioSpec products). Reservoir solution was 11% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5. Crystals were grown using the sitting drop vapor diffusion method at 20 C and appeared within 24 hours, reaching full size within 36 hours. Crystals were looped after one week.
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Resolution: 1.7→53.23 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.294 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.115 / 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
0.23379
3366
4.9 %
RANDOM
Rwork
0.1982
-
-
-
obs
0.19985
65737
99.58 %
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Solvent computation
Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parameters
Biso mean: 36.483 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.35 Å2
-0.4 Å2
-0.45 Å2
2-
-
0.32 Å2
0.25 Å2
3-
-
-
0.65 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→53.23 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4892
0
70
292
5254
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.017
5123
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.019
4741
X-RAY DIFFRACTION
r_angle_refined_deg
1.322
1.855
6956
X-RAY DIFFRACTION
r_angle_other_deg
1.092
2.698
10896
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.492
5
636
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.997
23.031
254
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.08
15
800
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.606
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.08
0.2
771
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
5915
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1229
X-RAY DIFFRACTION
r_mcbond_it
2.239
1.611
2544
X-RAY DIFFRACTION
r_mcbond_other
2.238
1.611
2542
X-RAY DIFFRACTION
r_mcangle_it
2.973
2.409
3180
X-RAY DIFFRACTION
r_mcangle_other
2.973
2.409
3180
X-RAY DIFFRACTION
r_scbond_it
3.432
1.953
2579
X-RAY DIFFRACTION
r_scbond_other
3.432
1.953
2579
X-RAY DIFFRACTION
r_scangle_other
4.848
2.791
3773
X-RAY DIFFRACTION
r_long_range_B_refined
7.246
20.31
5623
X-RAY DIFFRACTION
r_long_range_B_other
7.239
20.005
5576
LS refinement shell
Resolution: 1.7→1.744 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.37
257
-
Rwork
0.37
4638
-
obs
-
-
96.36 %
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
1.4095
-0.711
-0.2731
2.0501
0.6946
1.3763
0.0359
-0.0528
0.0341
0.0242
-0.0516
-0.0535
-0.0151
-0.045
0.0157
0.0887
-0.0881
-0.1121
0.1071
0.118
0.1505
12.935
0.334
0.662
2
1.6343
-0.5128
0.7498
0.9215
-0.431
2.1112
-0.0113
-0.0066
-0.0392
0.0068
-0.0053
0.0251
-0.0801
0.0467
0.0167
0.0862
-0.0675
-0.1111
0.076
0.1012
0.1552
-13.328
0.229
0.808
3
3.112
-0.9828
1.273
1.5077
-0.565
7.6469
0.0749
0.3142
0.5093
-0.0974
-0.1188
-0.1241
-1.0183
0.1419
0.044
0.2799
-0.0426
-0.0944
0.0666
0.0985
0.2684
-15.376
19.906
-5.518
4
2.3221
-0.6181
-1.3351
6.4411
3.3754
2.2343
-0.0375
-0.2427
-0.2646
0.5153
-0.0182
-0.0748
0.2715
0.08
0.0557
0.1563
-0.043
-0.0941
0.0951
0.1188
0.163
15.272
-19.002
8.625
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 402
2
X-RAY DIFFRACTION
2
B
1 - 404
3
X-RAY DIFFRACTION
3
C
0 - 14
4
X-RAY DIFFRACTION
4
D
0 - 14
+
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