Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.933 Å / Relative weight: 1
Reflection
Resolution: 1.9→48.3 Å / Num. obs: 56578 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.4
Reflection shell
Resolution: 1.9→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.4 / % possible all: 95.7
-
Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
SCALA
datascaling
MOLREP
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.27 Å / SU ML: 0.3 / σ(F): 1.28 / Phase error: 22.83 / Stereochemistry target values: ML Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORDS CONTAIN ISOTROPIC EQUIVALENTS OF THE SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
Rfactor
Num. reflection
% reflection
Rfree
0.234
5297
5 %
Rwork
0.196
-
-
obs
0.198
105612
90.5 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.69 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-2.6927 Å2
0.2268 Å2
-0.2884 Å2
2-
-
5.3277 Å2
6.3332 Å2
3-
-
-
-2.6351 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→48.27 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5298
0
70
374
5742
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
5509
X-RAY DIFFRACTION
f_angle_d
1.009
7523
X-RAY DIFFRACTION
f_dihedral_angle_d
14.678
1949
X-RAY DIFFRACTION
f_chiral_restr
0.076
859
X-RAY DIFFRACTION
f_plane_restr
0.005
972
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Number
Refine-ID
Type
Rms dev position (Å)
1
1
A
1292
X-RAY DIFFRACTION
POSITIONAL
1
2
C
1292
X-RAY DIFFRACTION
POSITIONAL
0.041
2
1
B
1326
X-RAY DIFFRACTION
POSITIONAL
2
2
D
1326
X-RAY DIFFRACTION
POSITIONAL
0.037
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.9-1.9216
0.2828
162
0.2753
3081
X-RAY DIFFRACTION
83
1.9216-1.9442
0.2916
165
0.2575
3198
X-RAY DIFFRACTION
87
1.9442-1.9679
0.2501
165
0.2543
3138
X-RAY DIFFRACTION
86
1.9679-1.9928
0.2674
179
0.2454
3321
X-RAY DIFFRACTION
89
1.9928-2.019
0.2765
166
0.2511
3183
X-RAY DIFFRACTION
86
2.019-2.0467
0.2922
173
0.2383
3232
X-RAY DIFFRACTION
90
2.0467-2.0759
0.28
176
0.2254
3267
X-RAY DIFFRACTION
87
2.0759-2.1069
0.222
173
0.2111
3297
X-RAY DIFFRACTION
90
2.1069-2.1399
0.223
175
0.2013
3308
X-RAY DIFFRACTION
88
2.1399-2.1749
0.2501
176
0.2012
3273
X-RAY DIFFRACTION
90
2.1749-2.2124
0.2278
164
0.2095
3305
X-RAY DIFFRACTION
89
2.2124-2.2527
0.2618
178
0.197
3283
X-RAY DIFFRACTION
91
2.2527-2.296
0.2703
186
0.1991
3413
X-RAY DIFFRACTION
90
2.296-2.3429
0.2488
165
0.1911
3289
X-RAY DIFFRACTION
90
2.3429-2.3938
0.2089
176
0.1785
3332
X-RAY DIFFRACTION
90
2.3938-2.4495
0.2558
178
0.19
3321
X-RAY DIFFRACTION
90
2.4495-2.5107
0.2309
180
0.1892
3412
X-RAY DIFFRACTION
91
2.5107-2.5786
0.2589
183
0.1848
3307
X-RAY DIFFRACTION
91
2.5786-2.6545
0.2375
179
0.1892
3396
X-RAY DIFFRACTION
92
2.6545-2.7402
0.2577
172
0.1838
3386
X-RAY DIFFRACTION
92
2.7402-2.8381
0.2348
185
0.1916
3443
X-RAY DIFFRACTION
92
2.8381-2.9517
0.2359
181
0.1866
3412
X-RAY DIFFRACTION
93
2.9517-3.086
0.2213
171
0.1907
3405
X-RAY DIFFRACTION
93
3.086-3.2487
0.2269
186
0.1802
3459
X-RAY DIFFRACTION
93
3.2487-3.4522
0.2086
172
0.1773
3441
X-RAY DIFFRACTION
93
3.4522-3.7186
0.1877
185
0.1629
3472
X-RAY DIFFRACTION
94
3.7186-4.0927
0.2111
184
0.1695
3469
X-RAY DIFFRACTION
95
4.0927-4.6845
0.1922
194
0.1603
3502
X-RAY DIFFRACTION
94
4.6845-5.9003
0.2145
185
0.1966
3506
X-RAY DIFFRACTION
95
5.9003-48.2834
0.226
183
0.2057
3464
X-RAY DIFFRACTION
94
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
0.8575
0.4534
0.0899
1.9442
0.2597
0.9272
0.0709
-0.0236
0.0336
0.0587
-0.0113
0.1193
-0.1231
-0.0608
-0
0.0643
0.0162
0.0088
0.0544
-0.0153
0.0781
14.2836
-2.715
6.2791
2
1.2309
0.1619
0.4369
0.8308
0.6624
1.2322
0.0401
-0.12
-0.0707
0.0769
0.0111
0.1063
0.1453
-0.0541
-0.0001
0.0955
-0.003
-0.0002
0.1258
0.0396
0.1498
12.6482
-15.4043
24.7593
3
1.1711
0.4768
0.456
1.4975
0.508
1.5409
0.0886
0.0745
-0.0659
-0.1017
-0.017
-0.0575
0.1489
0.1662
0.0001
0.0925
0.0386
0.0008
0.1115
0.0046
0.0926
-14.3369
12.4612
-25.8406
4
1.0325
0.5126
-0.2342
1.3992
-0.2452
0.5349
0.0641
-0.0297
-0.0118
0.169
-0.0176
-0.0582
-0.0036
0.1099
-0
0.0703
-0.0026
-0.0068
0.1411
-0.0112
0.0736
-12.6406
5.5066
-4.3003
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINA
2
X-RAY DIFFRACTION
2
CHAINB
3
X-RAY DIFFRACTION
3
CHAINC
4
X-RAY DIFFRACTION
4
CHAIND
+
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