Lysine-specificdemethylase6A / Histone demethylase UTX / Ubiquitously-transcribed TPR protein on the X chromosome / Ubiquitously- ...Histone demethylase UTX / Ubiquitously-transcribed TPR protein on the X chromosome / Ubiquitously-transcribed X chromosome tetratricopeptide repeat protein
Mass: 60264.375 Da / Num. of mol.: 1 / Fragment: UNP residues 880-1401 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM6A, UTX / Plasmid: pET47 / Production host: Escherichia coli (E. coli) References: UniProt: O15550, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
Method to determine structure: SAD / Resolution: 1.85→30.066 Å / FOM work R set: 0.8452 / SU ML: 0.22 / σ(F): 1.33 / Phase error: 22.23 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2179
2578
5.14 %
RANDOM
Rwork
0.1826
-
-
-
obs
0.1844
50150
-
-
Solvent computation
Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.672 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
4.5061 Å2
-0 Å2
-0 Å2
2-
-
-1.9859 Å2
-0 Å2
3-
-
-
-2.5202 Å2
Refinement step
Cycle: LAST / Resolution: 1.85→30.066 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3806
0
55
344
4205
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.003
4003
X-RAY DIFFRACTION
f_angle_d
0.811
5438
X-RAY DIFFRACTION
f_dihedral_angle_d
14.554
1485
X-RAY DIFFRACTION
f_chiral_restr
0.05
588
X-RAY DIFFRACTION
f_plane_restr
0.003
702
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
% reflection obs (%)
1.8501-1.8857
0.3054
127
0.2683
2033
75
1.8857-1.9242
0.3139
125
0.2601
2176
80
1.9242-1.966
0.2767
130
0.2512
2321
84
1.966-2.0118
0.2756
139
0.2297
2447
90
2.0118-2.0621
0.2719
120
0.2203
2575
94
2.0621-2.1178
0.2584
148
0.2095
2711
99
2.1178-2.1801
0.2642
154
0.2011
2755
100
2.1801-2.2505
0.2481
146
0.1977
2729
100
2.2505-2.3309
0.2186
147
0.1898
2750
100
2.3309-2.4241
0.2472
141
0.1889
2757
100
2.4241-2.5344
0.218
153
0.1933
2762
100
2.5344-2.668
0.2417
148
0.1816
2768
100
2.668-2.835
0.2123
161
0.1761
2764
100
2.835-3.0537
0.225
138
0.1832
2766
100
3.0537-3.3606
0.2301
142
0.19
2783
99
3.3606-3.8461
0.2164
165
0.1764
2773
99
3.8461-4.8424
0.1707
155
0.1409
2827
99
4.8424-30.0698
0.1817
139
0.1789
2875
96
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
0.3761
0.0765
-0.0132
0.1384
-0.0959
0.0718
0.2507
-0.0086
-0.0557
0.1703
-0.1058
-0.0344
0.0126
-0.0047
-0.0434
0.7187
0.1072
-0.0492
0.2973
0.0183
0.2596
41.4617
-26.0816
14.0518
2
0.2493
0.031
0.0869
1.106
0.2929
1.3276
-0.0395
-0.0011
-0.0247
-0.0018
-0.0865
-0.0389
-0.0843
-0.1272
0.0598
0.1617
0.0012
-0.0073
0.1969
-0.0073
0.1843
24.3796
6.7336
14.5248
3
1.2205
-0.1041
0.512
0.4318
-0.0783
0.7909
0.0938
0.2727
0.1851
0.0497
-0.1373
-0.0171
0.3518
0.1216
0.0015
0.2742
0.045
-0.0215
0.2518
0.012
0.2272
37.6221
-18.1879
-0.6569
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resseq886:927)
2
X-RAY DIFFRACTION
2
chain 'A' and (resseq928:1261)
3
X-RAY DIFFRACTION
3
chain 'A' and (resseq1262:1395)
+
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