- PDB-5gnb: Crystal Structure of the Receptor Binding Domain of the Spike Gly... -
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Basic information
Entry
Database: PDB / ID: 5gnb
Title
Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-CTD, 2.3 angstrom, native-SAD phasing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 2.08 Å / Relative weight: 1
Reflection
Resolution: 2.3→49.2 Å / Num. obs: 43316 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 89.76 % / Biso Wilson estimate: 31.062 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.23 / Net I/σ(I): 28.04
Reflection shell
Resolution: 2.3→2.36 Å / Redundancy: 30.92 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 3.37 / CC1/2: 0.894 / % possible all: 93.9
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Processing
Software
Name
Version
Classification
PHENIX
(1.10.1_2155: ???)
refinement
XDS
datareduction
XDS
datascaling
SHELXCD
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.3→49.2 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 23.97 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2192
2155
4.98 %
Random
Rwork
0.1728
-
-
-
obs
0.1751
43282
99.43 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parameters
Biso mean: 30.16 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→49.2 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2853
0
56
234
3143
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
3070
X-RAY DIFFRACTION
f_angle_d
0.854
4213
X-RAY DIFFRACTION
f_dihedral_angle_d
9.968
1859
X-RAY DIFFRACTION
f_chiral_restr
0.051
468
X-RAY DIFFRACTION
f_plane_restr
0.005
546
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.298-2.3515
0.3032
137
0.2349
2595
X-RAY DIFFRACTION
93
2.3515-2.4103
0.2566
140
0.2176
2720
X-RAY DIFFRACTION
99
2.4103-2.4754
0.2384
145
0.2056
2765
X-RAY DIFFRACTION
100
2.4754-2.5483
0.2889
141
0.1864
2762
X-RAY DIFFRACTION
100
2.5483-2.6305
0.2993
140
0.1831
2734
X-RAY DIFFRACTION
100
2.6305-2.7245
0.2113
148
0.1706
2760
X-RAY DIFFRACTION
100
2.7245-2.8336
0.2223
147
0.1732
2745
X-RAY DIFFRACTION
100
2.8336-2.9625
0.2372
144
0.1848
2731
X-RAY DIFFRACTION
100
2.9625-3.1187
0.2384
144
0.1914
2764
X-RAY DIFFRACTION
100
3.1187-3.3141
0.2323
143
0.1747
2762
X-RAY DIFFRACTION
100
3.3141-3.5699
0.1869
147
0.1637
2755
X-RAY DIFFRACTION
100
3.5699-3.929
0.2077
148
0.1545
2774
X-RAY DIFFRACTION
100
3.929-4.4972
0.2086
142
0.134
2741
X-RAY DIFFRACTION
100
4.4972-5.6647
0.1463
143
0.1508
2769
X-RAY DIFFRACTION
100
5.6647-49.2067
0.2302
146
0.1947
2750
X-RAY DIFFRACTION
100
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