Mass: 33365.621 Da / Num. of mol.: 1 Fragment: 3 N-terminal Immunoglobulin Domains (UNP residues 1-304) Source method: isolated from a genetically manipulated source Details: This structure represents the first three of four domains of Hoc from the bacteriophage RB49. Source: (gene. exp.) Enterobacteria phage RB49 (virus) / Gene: hoc / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Y442
Resolution: 1.95→1.98 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.28 / % possible all: 15
-
Processing
Software
Name
Version
Classification
Blu-Ice
datacollection
PHENIX
Autosol
modelbuilding
SOLVE
phasing
PHENIX
(phenix.refine: 1.7_650)
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
Autosol
phasing
Refinement
Method to determine structure: SIRAS, 3-wavelength data from a Pt derivative Resolution: 1.951→27.691 Å / SU ML: 0.32 / σ(F): 0 / σ(I): 0 / Phase error: 36.81 / Stereochemistry target values: ML Details: Diffraction data were anisotropic. Resolution of the dataset along the three principle mutually perpendicular directions determined by the vectors a*/|a*| + c*/|c*|; a*/|a*| - c*/|c*|, and ...Details: Diffraction data were anisotropic. Resolution of the dataset along the three principle mutually perpendicular directions determined by the vectors a*/|a*| + c*/|c*|; a*/|a*| - c*/|c*|, and b* was 1.95, 2.8 and 2.7 A, respectively (resolution at which average I/sigma = 2). The data were truncated using an ellipsoid which had its principle axes along these vectors. All reflections which were outside the ellipsoid and had I/sigma(I) < 2.0 were rejected. The structure factors were modified by applying an anisotropic scaling to scale up reflections located in the weak directions of reciprocal space. The components of the B-factor scaling tensor corresponding to the principle axes of the ellipsoid were 0, -60, -35 A2, respectively.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2673
1766
9.76 %
RANDOM
Rwork
0.2181
-
-
-
all
0.2231
35571
-
-
obs
0.2231
18095
50.87 %
-
Solvent computation
Shrinkage radii: 1.25 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.254 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-6.7957 Å2
0 Å2
-5.708 Å2
2-
-
-9.2991 Å2
0 Å2
3-
-
-
-4.9752 Å2
Refinement step
Cycle: LAST / Resolution: 1.951→27.691 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2333
0
1
90
2424
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
2376
X-RAY DIFFRACTION
f_angle_d
1.175
3238
X-RAY DIFFRACTION
f_dihedral_angle_d
14.301
840
X-RAY DIFFRACTION
f_chiral_restr
0.086
380
X-RAY DIFFRACTION
f_plane_restr
0.005
418
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.9511-2.0208
0.3074
48
0.2334
396
X-RAY DIFFRACTION
13
2.0208-2.1017
0.3195
44
0.249
522
X-RAY DIFFRACTION
16
2.1017-2.1973
0.3429
75
0.2819
715
X-RAY DIFFRACTION
23
2.1973-2.3131
0.4665
40
0.3999
383
X-RAY DIFFRACTION
12
2.3131-2.4579
0.3176
126
0.309
1161
X-RAY DIFFRACTION
37
2.4579-2.6476
0.374
163
0.3061
1635
X-RAY DIFFRACTION
51
2.6476-2.9138
0.3639
297
0.295
2716
X-RAY DIFFRACTION
85
2.9138-3.3348
0.3075
364
0.2583
3228
X-RAY DIFFRACTION
100
3.3348-4.1991
0.2677
250
0.197
2337
X-RAY DIFFRACTION
72
4.1991-27.6943
0.1929
359
0.1551
3236
X-RAY DIFFRACTION
97
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
0.5015
-0.0119
-0.2005
0.5788
-0.036
0.283
0.0364
-0.1132
0.0217
-0.0376
0.0185
0.1733
-0.0619
0.0084
0.0301
0.1619
-0.0112
-0.0561
0.0928
0.0577
0.3752
-38.9731
25.5143
-55.2805
2
0.1339
0.0001
0.238
0.3254
-0.1167
0.552
0.0567
-0.3923
-0.1358
-0.0149
0.0421
0.1224
0.0744
0.0486
-0.053
0.0351
0.0001
-0.1571
0.9518
0.2155
0.1568
-12.7528
15.4445
-28.8754
3
0.1359
-0.1349
-0.1597
0.2236
0.0501
0.5663
0.0485
-0.0526
0.0928
0.1086
-0.0069
-0.2658
-0.1236
0.3153
-0.0109
-0.0091
-0.1051
-0.0406
1.3264
-0.0766
0.2474
15.2963
25.1913
-2.0479
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and ((resseq2:89))
2
X-RAY DIFFRACTION
2
chain 'A' and ((resseq90:181))
3
X-RAY DIFFRACTION
3
chain 'A' and ((resseq182:304))
+
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