Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97935 Å / Relative weight: 1
Reflection
Resolution: 1.95→112.51 Å / Num. obs: 111077
Reflection shell
Resolution: 1.95→2 Å
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
PDB_EXTRACT
2
dataextraction
DNA
datacollection
XDS
datareduction
XSCALE
datascaling
SHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.95→112.51 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.172 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.201
5579
5 %
RANDOM
Rwork
0.168
-
-
-
obs
0.169
111007
91.75 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 35.864 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.07 Å2
0 Å2
0 Å2
2-
-
-0.04 Å2
0 Å2
3-
-
-
-0.03 Å2
Refinement step
Cycle: LAST / Resolution: 1.95→112.51 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9232
0
36
754
10022
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
r_bond_refined_d
0.016
X-RAY DIFFRACTION
r_bond_other_d
0.003
X-RAY DIFFRACTION
r_angle_refined_deg
1.465
X-RAY DIFFRACTION
r_angle_other_deg
0.59
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.023
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.023
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.295
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.4
X-RAY DIFFRACTION
r_chiral_restr
0.104
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
X-RAY DIFFRACTION
r_nbd_refined
0.224
X-RAY DIFFRACTION
r_nbd_other
0.198
X-RAY DIFFRACTION
r_nbtor_refined
0.3
X-RAY DIFFRACTION
r_nbtor_other
0.278
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.206
X-RAY DIFFRACTION
r_symmetry_vdw_refined
LS refinement shell
Resolution: 1.95→2 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.262
411
-
Rwork
0.188
8181
-
obs
-
8592
97.03 %
+
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