CarboxypeptidaseB2 / Carboxypeptidase U / CPU / Plasma carboxypeptidase B / pCPB / Thrombin-activable fibrinolysis inhibitor / TAFI
Mass: 45932.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: S58063 / Source: (gene. exp.) Homo sapiens (human) / Gene: CPB2 / Production host: Homo sapiens (human) / References: UniProt: Q96IY4, carboxypeptidase U
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.03324 Å / Relative weight: 1
Reflection
Resolution: 2.55→37.384 Å / Num. obs: 15499 / % possible obs: 96.2 % / Redundancy: 3 % / Net I/σ(I): 9.5
Reflection shell
Resolution: 2.55→2.66 Å / Num. unique obs: 1862
-
Processing
Software
Name
Version
Classification
REFMAC
5.8.0267
refinement
XDS
datareduction
XDS
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: in house model Resolution: 2.55→37.384 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.861 / SU B: 40.539 / SU ML: 0.385 / Cross valid method: FREE R-VALUE / ESU R: 0.852 / ESU R Free: 0.387 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.3156
773
5 %
Rwork
0.2543
14686
-
all
0.257
-
-
obs
-
15459
95.627 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 39.852 Å2
Baniso -1
Baniso -2
Baniso -3
1-
4.824 Å2
-0 Å2
-0 Å2
2-
-
-9.228 Å2
0 Å2
3-
-
-
4.404 Å2
Refinement step
Cycle: LAST / Resolution: 2.55→37.384 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3136
0
24
20
3180
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.013
3249
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
2908
X-RAY DIFFRACTION
r_angle_refined_deg
1.86
1.633
4434
X-RAY DIFFRACTION
r_angle_other_deg
1.263
1.569
6656
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.755
5
399
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.233
22.407
162
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.003
15
481
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.503
15
15
X-RAY DIFFRACTION
r_chiral_restr
0.075
0.2
433
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
3722
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
796
X-RAY DIFFRACTION
r_nbd_refined
0.223
0.2
717
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.204
0.2
2885
X-RAY DIFFRACTION
r_nbtor_refined
0.183
0.2
1506
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.085
0.2
1551
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.18
0.2
78
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.094
0.2
3
X-RAY DIFFRACTION
r_metal_ion_refined
0.253
0.2
3
X-RAY DIFFRACTION
r_nbd_other
0.166
0.2
23
X-RAY DIFFRACTION
r_mcbond_it
1.481
2.586
1599
X-RAY DIFFRACTION
r_mcbond_other
1.481
2.586
1598
X-RAY DIFFRACTION
r_mcangle_it
2.492
3.878
1997
X-RAY DIFFRACTION
r_mcangle_other
2.491
3.878
1998
X-RAY DIFFRACTION
r_scbond_it
1.365
2.65
1650
X-RAY DIFFRACTION
r_scbond_other
1.361
2.651
1649
X-RAY DIFFRACTION
r_scangle_it
2.333
3.933
2437
X-RAY DIFFRACTION
r_scangle_other
2.332
3.934
2438
X-RAY DIFFRACTION
r_lrange_it
4.053
29.351
3623
X-RAY DIFFRACTION
r_lrange_other
4.053
29.35
3623
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.55-2.616
0.443
64
0.397
1081
X-RAY DIFFRACTION
94.3941
2.616-2.688
0.376
62
0.376
1016
X-RAY DIFFRACTION
95.5674
2.688-2.766
0.488
46
0.391
1026
X-RAY DIFFRACTION
96.4029
2.766-2.851
0.492
48
0.382
986
X-RAY DIFFRACTION
97.1805
2.851-2.945
0.467
49
0.357
984
X-RAY DIFFRACTION
96.9043
2.945-3.048
0.42
53
0.314
937
X-RAY DIFFRACTION
96.5854
3.048-3.163
0.375
52
0.319
901
X-RAY DIFFRACTION
96.8496
3.163-3.292
0.377
22
0.322
874
X-RAY DIFFRACTION
95.8289
3.292-3.438
0.365
45
0.295
827
X-RAY DIFFRACTION
95.719
3.438-3.606
0.319
44
0.266
832
X-RAY DIFFRACTION
97.6589
3.606-3.801
0.301
32
0.223
759
X-RAY DIFFRACTION
95.9951
3.801-4.031
0.283
44
0.206
704
X-RAY DIFFRACTION
95.4082
4.031-4.31
0.269
38
0.194
670
X-RAY DIFFRACTION
94.9062
4.31-4.655
0.29
42
0.15
618
X-RAY DIFFRACTION
95.5137
4.655-5.098
0.178
33
0.152
586
X-RAY DIFFRACTION
95.2308
5.098-5.699
0.203
30
0.157
529
X-RAY DIFFRACTION
94.7458
5.699-6.58
0.245
24
0.201
465
X-RAY DIFFRACTION
93.858
6.58-8.055
0.314
16
0.194
406
X-RAY DIFFRACTION
92.1397
8.055-11.376
0.227
17
0.172
312
X-RAY DIFFRACTION
93.7322
11.376-37.384
0.233
12
0.233
173
X-RAY DIFFRACTION
85.6481
Refinement TLS params.
Method: refined / Origin x: 7.8915 Å / Origin y: 20.8976 Å / Origin z: 18.699 Å
11
12
13
21
22
23
31
32
33
T
0.0084 Å2
-0.0228 Å2
0.0021 Å2
-
0.5765 Å2
0.0017 Å2
-
-
0.0055 Å2
L
0.4671 °2
-0.0895 °2
-0.0781 °2
-
0.0194 °2
0.0461 °2
-
-
0.5264 °2
S
-0.0474 Å °
0.017 Å °
-0.0428 Å °
0.0062 Å °
0.0117 Å °
0.01 Å °
-0.0311 Å °
0.0153 Å °
0.0357 Å °
Refinement TLS group
Selection: ALL
+
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