ComplementfactorH / H factor 1 / Coordinate model: Cα atoms only
Mass: 137188.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Purified from pooled plasma / Source: (natural) Homo sapiens (human) / References: UniProt: P08603
Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Soln scatter
Type: x-ray Buffer name: 250 MM NACL 2.7 MM KCL 8.1 MM NAH2PO4 1.5 MM KH2PO4 Conc. range: 0.4 mg/ml / Data analysis software list: SCTPL7, GNOM / Data reduction software list: MULTICCD / Detector type: FRELON CCD CAMERA / Max mean cross sectional radii gyration: 1.52 nm / Max mean cross sectional radii gyration esd: 0.09 nm / Mean guiner radius: 9.22 nm / Mean guiner radius esd: 0.56 nm / Min mean cross sectional radii gyration: 2.31 nm / Min mean cross sectional radii gyration esd: 0.09 nm / Num. of time frames: 10 / Protein length: 1 / Sample pH: 7.4 / Source beamline: IDO2 / Source class: Y / Source type: ESRF GRENOBLE / Temperature: 293 K
-
Processing
Software
Name
Version
Classification
SCTPL7
modelbuilding
GNOM
modelbuilding
Insight II
II98
modelbuilding
SCTPL7
phasing
GNOM
phasing
Refinement
Method to determine structure: CONSTRAINED SCATTERING MODELLING Details: THE COORDINATES CONTAIN ONLY CA ATOMS.
Refinement step
Cycle: LAST
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1213
0
0
0
1213
Soln scatter model
Conformer selection criteria: STRUCTURES WITH THE LOWEST GOODNESS-OF-FIT R-FACTOR AFTER FILTERING ON RG AND RXS-1 Num. of conformers calculated: 5000 / Num. of conformers submitted: 8 / Representative conformer: 1 / Software list: INSIGHT II, SCTPL7, GNOM
+
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