Mass: 62110.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NECK + MOTOR DOMAIN OF KIF2C FUSED TO THE A-C2 DARPIN Source: (gene. exp.) Homo sapiens (human) / Gene: KIF2C, KNSL6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99661
FOR BETA-TUBULIN, THERE ARE THREE MAJOR ISOTYPES EXPRESSED IN THE BRAIN (BANERJEE AT AL, JBC 1988, ...FOR BETA-TUBULIN, THERE ARE THREE MAJOR ISOTYPES EXPRESSED IN THE BRAIN (BANERJEE AT AL, JBC 1988, VOL 263:3029-34). THE BETA 2B ISOTYPE SEQUENCE WAS USED BUT POINT MUTATIONS WERE INTRODUCED WHEN POSSIBLE TO TAKE THE ISOTYPE DIVERSITY INTO ACCOUNT.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 40 mM Pipes-K pH 6.8 4% PEG3350
Resolution: 3.19→42.91 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.874 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.666 Details: THE DEBYE AND STARANISO PROGAMS DEVELOPPED BY GLOBAL PHASING LTD. WERE APPLIED TO THE AIMLESS SCALED DATA WITHOUT TRUNCATION OF THE RESOLUTION. THESE CORRECTED ANISOTROPIC AMPLITUDES WERE ...Details: THE DEBYE AND STARANISO PROGAMS DEVELOPPED BY GLOBAL PHASING LTD. WERE APPLIED TO THE AIMLESS SCALED DATA WITHOUT TRUNCATION OF THE RESOLUTION. THESE CORRECTED ANISOTROPIC AMPLITUDES WERE USED FOR FURTHER CYCLES OF REFINEMENTS WITH BUSTER.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.257
1009
5.07 %
RANDOM
Rwork
0.211
-
-
-
obs
0.213
19903
66.3 %
-
Displacement parameters
Biso mean: 104.06 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-7.1419 Å2
0 Å2
0 Å2
2-
-
10.4242 Å2
0 Å2
3-
-
-
-3.2823 Å2
Refine analyze
Luzzati coordinate error obs: 0.48 Å
Refinement step
Cycle: 1 / Resolution: 3.19→42.91 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
10299
0
122
0
10421
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
10635
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.1
14426
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
3692
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
268
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
1606
HARMONIC
5
X-RAY DIFFRACTION
t_it
10635
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
2
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
3
X-RAY DIFFRACTION
t_other_torsion
18.14
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
1393
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
12613
SEMIHARMONIC
4
LS refinement shell
Resolution: 3.19→3.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
Rfactor
Num. reflection
% reflection
Rfree
0.255
-
5.37 %
Rwork
0.244
952
-
all
0.244
1006
-
obs
-
-
23.41 %
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
1.2237
0.1731
-0.074
2.3901
-0.3306
1.4461
-0.0445
-0.1454
-0.376
-0.0964
0.0514
0.034
0.1865
-0.0439
-0.007
0.9473
-0.2636
0.0703
0.6127
-0.0546
0.4562
-24.8932
-76.0274
31.1859
2
1.1496
0.0699
-0.1414
3.1118
-0.4513
2.0759
0.0311
0.088
0.1076
-0.3806
0.0734
-0.0445
-0.0041
-0.0635
-0.1045
1.1898
-0.313
0.0353
0.5621
-0.0608
0.2755
-14.0661
-37.6042
16.7912
3
1.4017
-0.3514
-0.1055
3.4938
-0.9148
2.4948
-0.2946
-0.1637
0.199
0.1556
0.2909
0.246
-0.1498
-0.2839
0.0037
1.0783
-0.1252
-0.0056
0.5642
-0.1203
0.1716
-32.3371
-35.3119
54.3047
4
4.1802
-0.5011
-1.1282
8.1341
-3.4748
5.5532
0.0378
0.0142
0.4924
0.1275
0.0103
-0.6574
-0.2271
0.2255
-0.0481
1.2806
-0.334
0.029
0.6968
-0.1125
0.5399
0.2437
-2.1071
25.2663
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ A|* }
2
X-RAY DIFFRACTION
2
{ B|* }
3
X-RAY DIFFRACTION
3
{ C|227:588800:801 }
4
X-RAY DIFFRACTION
4
{ C|622:744 }
+
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