regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding ...regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / vitamin D receptor signaling pathway / positive regulation of vitamin D receptor signaling pathway / bile acid signaling pathway / intestinal absorption / mammary gland branching involved in pregnancy / decidualization / negative regulation of keratinocyte proliferation / positive regulation of bone mineralization / nuclear retinoid X receptor binding / lactation / skeletal system development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / cell morphogenesis / Nuclear Receptor transcription pathway / intracellular calcium ion homeostasis / RNA polymerase II transcription regulator complex / nuclear receptor activity / calcium ion transport / cell differentiation / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function
Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.377 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19897
3652
5 %
RANDOM
Rwork
0.1792
-
-
-
all
0.18018
68780
-
-
obs
0.18018
68780
95.12 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 17.054 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.52 Å2
0 Å2
0 Å2
2-
-
0.16 Å2
0 Å2
3-
-
-
0.36 Å2
Refinement step
Cycle: LAST / Resolution: 1.3→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2017
0
35
275
2327
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
2127
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1476
X-RAY DIFFRACTION
r_angle_refined_deg
1.297
2.004
2888
X-RAY DIFFRACTION
r_angle_other_deg
0.859
3
3623
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.864
5
262
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.53
24.066
91
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.451
15
391
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.251
15
14
X-RAY DIFFRACTION
r_chiral_restr
0.067
0.2
332
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
2299
X-RAY DIFFRACTION
r_gen_planes_other
0.005
0.02
402
LS refinement shell
Resolution: 1.301→1.334 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.249
205
-
Rwork
0.241
4299
-
obs
-
-
84.05 %
Refinement TLS params.
Method: refined / Origin x: -13.3956 Å / Origin y: -5.4449 Å / Origin z: 24.2584 Å
11
12
13
21
22
23
31
32
33
T
0.0159 Å2
0 Å2
-0.0083 Å2
-
0.0053 Å2
0.0043 Å2
-
-
0.0185 Å2
L
0.5191 °2
0.171 °2
0.3059 °2
-
0.3719 °2
0.0898 °2
-
-
0.6878 °2
S
-0.0172 Å °
0.0376 Å °
0.0485 Å °
-0.036 Å °
-0.0083 Å °
0.0056 Å °
-0.0133 Å °
-0.0005 Å °
0.0255 Å °
+
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