Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
-
Details
Sequence details
THE CRYSTALLIZED SEQUENCE CORRESPONDS TO THE HUMAN MENIN ISOFORM 2
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal grow
Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data ...Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution: 1.63→38.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.534 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19396
3087
5.1 %
RANDOM
Rwork
0.16269
-
-
-
obs
0.16425
57894
99.04 %
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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: 24.078 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.06 Å2
-0 Å2
-0 Å2
2-
-
0.27 Å2
-0 Å2
3-
-
-
-0.21 Å2
Refinement step
Cycle: LAST / Resolution: 1.63→38.14 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3657
0
76
373
4106
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.019
3887
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.02
3697
X-RAY DIFFRACTION
r_angle_refined_deg
1.822
1.976
5274
X-RAY DIFFRACTION
r_angle_other_deg
1.07
3.006
8475
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.89
5
482
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.628
23.563
174
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.521
15
629
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.786
15
27
X-RAY DIFFRACTION
r_chiral_restr
0.115
0.2
587
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
4395
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
916
X-RAY DIFFRACTION
r_mcbond_it
2.836
1.995
1909
X-RAY DIFFRACTION
r_mcbond_other
2.797
1.997
1909
X-RAY DIFFRACTION
r_mcangle_it
3.504
3.111
2390
X-RAY DIFFRACTION
r_mcangle_other
3.515
3.118
2391
X-RAY DIFFRACTION
r_scbond_it
4.383
3.211
1978
X-RAY DIFFRACTION
r_scbond_other
4.379
3.208
1978
X-RAY DIFFRACTION
r_scangle_other
5.754
4.495
2882
X-RAY DIFFRACTION
r_long_range_B_refined
8.894
9.5
4861
X-RAY DIFFRACTION
r_long_range_B_other
8.893
9.505
4862
LS refinement shell
Resolution: 1.63→1.672 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.251
220
-
Rwork
0.227
4191
-
obs
-
-
98.13 %
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
2.1169
1.1421
-0.2935
2.5787
-1.0763
1.5421
-0.0469
-0.0916
-0.2885
-0.1496
-0.0083
-0.1321
0.3791
0.2477
0.0552
0.2844
0.0524
0.0026
0.1629
0.0339
0.3131
-4.486
-10.364
1.2
2
1.3407
0.3742
0.0137
0.6682
-0.2696
1.1239
0.0596
-0.1818
-0.0107
0.0122
-0.0512
-0.0068
0.1155
-0.0264
-0.0083
0.15
-0.0081
-0.0102
0.0533
0.0002
0.1733
-12.783
-3.403
6.029
3
7.5219
4.0018
-3.5999
8.0163
-5.969
4.5245
-0.5641
-0.2103
-0.781
-1.0086
0.321
-0.2199
0.8311
-0.1972
0.2431
0.6091
-0.1549
-0.1467
0.0657
0.0786
0.4848
-29.85
-16.641
-10.916
4
0.6168
-0.1298
0.1706
0.2355
0.0717
0.5439
0.0199
-0.0693
0.0128
0.0183
0.0203
0.0285
0.0974
-0.0881
-0.0402
0.1731
-0.0295
-0.0073
0.0705
0.0063
0.2008
-24.197
-0.371
-8.86
5
1.1251
0.031
0.1766
1.2818
-0.5197
1.7441
0.0273
0.0506
0.0993
-0.1051
-0.0071
0.1073
0.069
-0.0742
-0.0202
0.1584
-0.0192
-0.0066
0.0282
-0.0082
0.2047
-21.988
4.581
-20.799
6
0.3214
-0.0294
0.2137
0.3617
-0.3078
1.0282
-0.0198
-0.001
0.0622
0.0338
-0.0695
-0.0748
-0.026
0.1537
0.0893
0.1286
-0.0053
-0.0047
0.0453
0.0061
0.2097
-2.536
10.923
-12.017
7
0.5472
0.2262
-0.0241
0.6931
-0.069
0.5954
-0.0303
-0.0529
-0.0039
-0.0314
-0.0148
-0.008
-0.0014
0.0458
0.0451
0.1635
-0.0026
-0.0062
0.0714
0.0066
0.23
-10.033
27.783
-22.101
8
2.7716
1.7283
-1.7724
1.5761
-0.69
1.5837
-0.0768
0.0473
0.0247
-0.1009
0.061
0.0384
-0.1035
-0.0558
0.0158
0.198
0.012
-0.0126
0.09
0.0146
0.2408
-9.892
36.634
-27.493
9
1.4553
-0.5399
0.3705
4.2712
0.5419
0.4037
-0.074
0.082
0.1693
-0.0497
0.0414
-0.3059
-0.1173
0.0458
0.0326
0.188
0.0117
-0.0446
0.0399
0.0062
0.2175
-12.965
36.673
-33.379
10
30.9854
-10.0964
2.6103
54.8602
-9.252
1.5917
-0.3107
-2.2213
-0.6187
1.3353
0.2183
-1.0648
-0.228
-0.1317
0.0923
0.5323
0.0433
-0.0337
0.3539
0.1426
0.423
-29.251
44.617
-29.468
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 30
2
X-RAY DIFFRACTION
2
A
31 - 97
3
X-RAY DIFFRACTION
3
A
98 - 111
4
X-RAY DIFFRACTION
4
A
112 - 202
5
X-RAY DIFFRACTION
5
A
203 - 235
6
X-RAY DIFFRACTION
6
A
236 - 336
7
X-RAY DIFFRACTION
7
A
337 - 428
8
X-RAY DIFFRACTION
8
A
429 - 460
9
X-RAY DIFFRACTION
9
A
461 - 580
10
X-RAY DIFFRACTION
10
A
581 - 588
+
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