Mass: 18.015 Da / Num. of mol.: 461 / 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
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.27 Å3/Da / Density % sol: 45.91 %
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: 1.45→38.48 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.612 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.18856
4372
5 %
RANDOM
Rwork
0.16158
-
-
-
obs
0.16295
82790
99.86 %
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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: 25.065 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.59 Å2
-0 Å2
0 Å2
2-
-
0.37 Å2
-0 Å2
3-
-
-
0.22 Å2
Refinement step
Cycle: LAST / Resolution: 1.45→38.48 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3686
0
92
461
4239
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.019
3914
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.02
3742
X-RAY DIFFRACTION
r_angle_refined_deg
1.996
1.98
5297
X-RAY DIFFRACTION
r_angle_other_deg
1.178
3.008
8597
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.828
5
479
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.76
24.011
177
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.716
15
644
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.975
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.211
0.2
587
X-RAY DIFFRACTION
r_gen_planes_refined
0.011
0.02
4390
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
903
X-RAY DIFFRACTION
r_mcbond_it
2.642
1.754
1904
X-RAY DIFFRACTION
r_mcbond_other
2.642
1.754
1904
X-RAY DIFFRACTION
r_mcangle_it
3.356
2.733
2383
X-RAY DIFFRACTION
r_mcangle_other
3.356
2.74
2384
X-RAY DIFFRACTION
r_scbond_it
5.154
3.116
2010
X-RAY DIFFRACTION
r_scbond_other
5.153
3.117
2010
X-RAY DIFFRACTION
r_scangle_other
6.251
4.278
2913
X-RAY DIFFRACTION
r_long_range_B_refined
9.04
9.199
4899
X-RAY DIFFRACTION
r_long_range_B_other
9.04
9.21
4900
LS refinement shell
Resolution: 1.452→1.49 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.277
344
-
Rwork
0.21
5944
-
obs
-
-
98.45 %
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
1.6864
-0.9511
-0.5758
2.8266
1.6333
1.6991
-0.0183
0.0906
-0.2497
0.0785
0.0064
0.0935
0.3232
-0.1146
0.0118
0.4769
-0.0311
-0.0135
0.1011
-0.0246
0.1708
4.555
-10.355
-1.232
2
1.2933
-0.1094
0.0972
0.5835
0.1276
1.2835
0.0385
0.1814
-0.0027
-0.0063
-0.0173
0.0315
0.0544
0.0127
-0.0211
0.3561
0.002
-0.0087
0.0367
-0.0055
0.055
12.914
-3.392
-6.064
3
2.2043
-1.2905
-0.9525
4.2311
1.9802
0.9949
-0.2255
0.0339
-0.3472
0.3632
0.1441
0.1256
0.2056
0.0721
0.0814
0.5868
0.0808
-0.0321
0.0771
-0.0459
0.2015
30.588
-16.604
10.61
4
1.0109
-0.5209
0.4425
1.1241
-0.1794
0.7033
-0.0052
0.1384
0.1091
-0.0395
-0.0519
-0.1343
-0.0017
0.2371
0.0571
0.417
-0.0066
-0.0072
0.0827
0.0077
0.1029
29.669
-0.955
6.862
5
0.4593
0.0678
0.3037
0.3745
0.0143
0.8942
0.0197
0.0421
0.0111
0.0099
0.0125
-0.0394
0.0801
0.0809
-0.0322
0.3676
0.0238
-0.0085
0.0291
-0.0042
0.0907
22.997
1.82
13.8
6
1.4774
-0.3071
0.9612
0.4408
-0.2913
1.6621
-0.0263
0.055
0.1637
-0.0008
-0.0429
-0.0208
-0.0678
-0.0396
0.0692
0.3685
0.0104
-0.0038
0.0227
-0.0003
0.0953
7.708
5.469
3.609
7
0.3647
0.1284
0.3245
0.9991
0.513
1.0322
-0.0229
0.0042
0.0342
-0.0199
-0.0615
0.0979
-0.0082
-0.1075
0.0844
0.3434
0.0009
0.0048
0.0277
-0.0124
0.0895
3.055
12.839
17.605
8
1.3141
-1.0988
1.158
3.775
-0.0423
3.9472
0.119
0.2079
0.0362
-0.1788
-0.107
-0.2502
0.0554
0.3019
-0.012
0.3838
0.0047
0.0283
0.0562
0.0013
0.1461
22.622
19.673
18.445
9
0.3706
-0.3267
-0.031
0.7348
0.0473
0.8181
-0.011
0.0325
0.0107
0.036
-0.0192
0.0161
-0.0846
-0.0333
0.0302
0.3958
-0.0028
-0.006
0.0531
-0.0019
0.1184
8.713
33.191
25.782
10
3.1928
1.5081
1.606
1.8703
0.1709
1.1074
-0.1987
0.004
0.202
-0.2922
0.1668
0.2551
-0.0232
-0.0727
0.0319
0.5102
-0.039
-0.0653
0.0315
0.016
0.1293
18.796
42.841
30.691
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 - 109
4
X-RAY DIFFRACTION
4
A
110 - 137
5
X-RAY DIFFRACTION
5
A
138 - 228
6
X-RAY DIFFRACTION
6
A
229 - 264
7
X-RAY DIFFRACTION
7
A
265 - 351
8
X-RAY DIFFRACTION
8
A
352 - 363
9
X-RAY DIFFRACTION
9
A
364 - 561
10
X-RAY DIFFRACTION
10
A
562 - 588
+
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