mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding / positive regulation of germinal center formation ...mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding / positive regulation of germinal center formation / negative regulation of adenosine receptor signaling pathway / histamine secretion / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / inosine biosynthetic process / amide catabolic process / adenosine deaminase / hypoxanthine biosynthetic process / germinal center B cell differentiation / adenosine catabolic process / adenosine deaminase activity / inhibition of non-skeletal tissue mineralization / hypoxanthine salvage / deoxyadenosine catabolic process / dAMP catabolic process / adenosine metabolic process / positive regulation of T cell differentiation in thymus / AMP catabolic process / dATP catabolic process / mucus secretion / negative regulation of leukocyte migration / regulation of cell-cell adhesion mediated by integrin / response to purine-containing compound / embryonic digestive tract development / allantoin metabolic process / trophectodermal cell differentiation / GMP salvage / IMP salvage / positive regulation of smooth muscle contraction / Peyer's patch development / germinal center formation / negative regulation of mature B cell apoptotic process / AMP salvage / regulation of T cell differentiation in thymus / negative regulation of thymocyte apoptotic process / anchoring junction / positive regulation of alpha-beta T cell differentiation / alpha-beta T cell differentiation / positive regulation of T cell differentiation / regulation of T cell differentiation / positive regulation of heart rate / leukocyte migration / lung alveolus development / positive regulation of T cell receptor signaling pathway / thymocyte apoptotic process / B cell proliferation / T cell differentiation / smooth muscle contraction / : / response to vitamin E / positive regulation of calcium-mediated signaling / positive regulation of B cell proliferation / T cell activation / dendrite cytoplasm / liver development / calcium-mediated signaling / lung development / placenta development / negative regulation of inflammatory response / positive regulation of T cell activation / T cell receptor signaling pathway / T cell differentiation in thymus / in utero embryonic development / lysosome / cell adhesion / response to hypoxia / external side of plasma membrane / neuronal cell body / apoptotic process / negative regulation of apoptotic process / extracellular space / zinc ion binding / cytoplasm / cytosol Similarity search - Function
Resolution: 2→37.48 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.791 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22308
2433
5.1 %
RANDOM
Rwork
0.20199
-
-
-
all
0.2031
-
-
-
obs
0.2031
45618
90.79 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 28.619 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.77 Å2
0 Å2
1.12 Å2
2-
-
-1.31 Å2
0 Å2
3-
-
-
-0.18 Å2
Refinement step
Cycle: LAST / Resolution: 2→37.48 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5576
0
40
356
5972
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
5744
X-RAY DIFFRACTION
r_angle_refined_deg
1.675
1.974
7778
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.757
5
696
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.933
24.667
270
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.782
15
1018
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.521
15
30
X-RAY DIFFRACTION
r_chiral_restr
0.194
0.2
850
X-RAY DIFFRACTION
r_gen_planes_refined
0.017
0.021
4342
X-RAY DIFFRACTION
r_mcbond_it
1.527
1.5
3480
X-RAY DIFFRACTION
r_mcangle_it
2.469
2
5634
X-RAY DIFFRACTION
r_scbond_it
4.241
3
2264
X-RAY DIFFRACTION
r_scangle_it
6.377
4.5
2144
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.298
163
-
Rwork
0.279
3129
-
obs
-
3129
84.37 %
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi