A: Granzyme H B: Granzyme H C: Granzyme H D: Granzyme H E: Granzyme H F: Granzyme H G: Granzyme H H: Granzyme H I: Granzyme H J: Granzyme H K: Granzyme H L: Granzyme H hetero molecules
Monochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal), indirect water cooling (2nd crystal) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Resolution: 3→39.8 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.854 / SU B: 54.981 / SU ML: 0.436 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 2. THE ELECTRON DENSITY MAP FOR CHAIN L IS VERY WEAK
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.30593
3931
5 %
RANDOM
Rwork
0.27069
-
-
-
obs
0.27249
74302
99.8 %
-
all
-
74438
-
-
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: 70.066 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.61 Å2
0 Å2
-0 Å2
2-
-
0.23 Å2
-0 Å2
3-
-
-
1.38 Å2
Refinement step
Cycle: LAST / Resolution: 3→39.8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
21176
0
78
38
21292
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.019
21759
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.867
1.968
29410
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.554
5
2690
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.111
23.063
862
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
21.053
15
3939
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.391
15
156
X-RAY DIFFRACTION
r_chiral_restr
0.117
0.2
3225
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
16087
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 3→3.077 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.448
267
-
Rwork
0.389
5001
-
obs
-
-
99.79 %
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
2.0004
1.0622
-0.9167
1.2955
-1.0789
0.9649
-0.2389
0.4227
-0.3298
-0.0983
-0.0129
-0.0836
-0.0409
0.0308
0.2519
0.5499
-0.1005
-0.028
0.2798
0.0597
0.8142
-64.1267
86.3975
-17.8954
2
3.0467
-0.5759
0.9019
3.4775
-0.8863
2.5483
-0.1714
-0.0638
0.2176
-0.1069
0.0603
-0.1557
0.0128
-0.0509
0.1111
0.3765
0.0091
-0.0329
0.3243
0.127
0.2164
29.4139
60.6087
15.8664
3
1.2211
-0.7742
0.1083
2.7032
1.4539
1.1881
-0.3262
-0.2841
0.2749
-0.0823
0.0062
-0.0827
-0.1086
-0.2397
0.32
0.4233
0.0846
-0.0689
0.6525
-0.2355
0.6823
-56.2085
30.9688
15.7626
4
0.8912
-0.1559
0.013
2.1347
1.2364
2.3059
-0.3678
0.0004
0.2276
0.0616
0.3709
0.3955
0.0569
0.5972
-0.0031
0.3691
0.0836
-0.0585
0.8511
0.0733
0.2199
56.5877
61.4436
-13.882
5
1.3492
1.2502
0.5834
2.4366
1.1694
0.7747
-0.5515
-0.3948
-0.0702
-0.3939
0.4689
0.3236
-0.1015
0.2284
0.0825
0.5201
0.1777
-0.0582
0.8708
0.1317
0.3267
64.4942
6.0303
13.5111
6
1.9549
-0.8368
0.7344
4.6464
-1.06
1.6132
-0.225
-0.0131
-0.0039
0.505
0.36
0.1162
-0.1718
-0.1392
-0.135
0.4026
0.0339
-0.03
0.2811
0.1082
0.3412
21.2783
5.116
-10.3616
7
2.3732
1.8816
-0.9794
2.6088
-1.387
1.4622
-0.325
0.2149
-0.046
-0.3448
0.397
0.2921
-0.0301
-0.0626
-0.072
0.4644
-0.0843
-0.1945
0.41
0.271
0.4648
11.334
30.2334
25.8291
8
1.0083
-1.212
-0.9248
2.2541
1.5221
1.1446
-0.5092
-0.3042
0.1571
0.2719
0.782
-0.1145
0.2365
0.4679
-0.2728
0.5854
0.4541
-0.1587
1.3166
-0.2091
0.3239
74.8135
31.7135
-23.6996
9
2.2437
0.5075
0.0279
2.8573
-1.7713
1.9285
-0.1833
0.3615
0.5327
0.084
-0.0422
-0.1077
0.0694
-0.3107
0.2255
0.3736
-0.0137
-0.1645
0.3038
0.0831
0.6416
-28.9305
30.065
-15.8931
10
1.2976
1.0568
0.8834
1.2621
1.0593
1.1316
-0.594
0.0335
0.3363
-0.288
0.1657
0.6852
-0.1684
0.4189
0.4283
0.6074
0.0557
-0.4465
0.3536
0.1862
1.2703
-10.1329
59.9744
-5.2997
11
2.2753
-2.4027
1.2507
2.6121
-1.3704
1.4159
-1.0601
-0.5005
1.2642
0.9501
0.4805
-1.4762
-0.1929
-1.2138
0.5795
0.677
-0.0637
-0.7187
1.444
-0.5407
1.2645
-74.0272
61.5137
6.2677
12
5.6178
-1.6796
-0.85
5.2095
2.0406
2.531
-0.2446
-0.5654
-0.1499
0.2491
-0.155
1.6503
-0.293
-0.2544
0.3997
1.0002
0.1098
-0.1346
0.4155
0.0626
1.78
-20.7642
85.6196
17.7302
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
16 - 304
2
X-RAY DIFFRACTION
2
B
16 - 403
3
X-RAY DIFFRACTION
3
C
16 - 301
4
X-RAY DIFFRACTION
4
D
16 - 406
5
X-RAY DIFFRACTION
5
E
16 - 404
6
X-RAY DIFFRACTION
6
F
16 - 404
7
X-RAY DIFFRACTION
7
G
16 - 301
8
X-RAY DIFFRACTION
8
H
16 - 301
9
X-RAY DIFFRACTION
9
I
16 - 408
10
X-RAY DIFFRACTION
10
J
16 - 301
11
X-RAY DIFFRACTION
11
K
16 - 302
12
X-RAY DIFFRACTION
12
L
16 - 404
+
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