MHC class I protein binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signal transduction / extracellular exosome / plasma membrane Similarity search - Function
Resolution: 1.6→1.66 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.92 / Num. unique all: 1289 / Rsym value: 0.28 / % possible all: 92.8
-
Processing
Software
Name
Version
Classification
Blu-Ice
datacollection
AMoRE
phasing
PHENIX
(phenix.refine: 1.5_2)
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.07 Å / SU ML: 0.2 / σ(F): 0.13 / Phase error: 20.68 / Stereochemistry target values: ML Details: The starting model is obtained by single isomorphous replacement with a iodine derivative data.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2249
671
4.93 %
Random
Rwork
0.198
-
-
-
obs
0.1994
13610
96.35 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.577 Å2 / ksol: 0.416 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
7.8691 Å2
-0 Å2
-0 Å2
2-
-
-5.0388 Å2
0 Å2
3-
-
-
-2.8302 Å2
Refinement step
Cycle: LAST / Resolution: 1.6→33.07 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
994
0
0
130
1124
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.005
1024
X-RAY DIFFRACTION
f_angle_d
0.959
1385
X-RAY DIFFRACTION
f_dihedral_angle_d
17.895
370
X-RAY DIFFRACTION
f_chiral_restr
0.065
140
X-RAY DIFFRACTION
f_plane_restr
0.003
177
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
% reflection obs (%)
1.6-1.7236
0.2392
120
0.2073
2346
89
1.7236-1.8971
0.2532
127
0.1944
2558
97
1.8971-2.1715
0.2064
140
0.1846
2635
99
2.1715-2.7357
0.2355
131
0.1948
2690
100
2.7357-33.0766
0.2152
153
0.1948
2710
97
Refinement TLS params.
Method: refined / Origin x: 10.198 Å / Origin y: -8.3398 Å / Origin z: -6.4539 Å
11
12
13
21
22
23
31
32
33
T
0.0881 Å2
-0.0036 Å2
0.0086 Å2
-
0.1003 Å2
0.002 Å2
-
-
0.0978 Å2
L
0.7771 °2
-0.3382 °2
-0.2369 °2
-
0.6812 °2
0.1821 °2
-
-
1.3328 °2
S
0.0154 Å °
0.036 Å °
-0.0148 Å °
-0.0563 Å °
-0.0328 Å °
0.0046 Å °
-0.1661 Å °
-0.0038 Å °
-0 Å °
Refinement TLS group
Selection details: all
+
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