porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / porphyrin-containing compound metabolic process / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process ...porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / porphyrin-containing compound metabolic process / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / nucleoplasm / cytosol Similarity search - Function
Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 18, 2008 / Details: yale mirrors
Radiation
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Av σ(I) over netI: 15.35 / Number: 135250 / Rmerge(I) obs: 0.11 / Χ2: 1.03 / D res high: 2.2 Å / D res low: 40 Å / Num. obs: 22288 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
4.74
40
96.1
1
0.069
1.285
3.76
4.74
99
1
0.086
1.39
3.29
3.76
99.8
1
0.103
1.086
2.99
3.29
99.8
1
0.138
1.078
2.77
2.99
100
1
0.176
0.937
2.61
2.77
99.9
1
0.227
0.952
2.48
2.61
99.9
1
0.273
0.858
2.37
2.48
100
1
0.31
0.81
2.28
2.37
99.9
1
0.373
0.842
2.2
2.28
98.6
1
0.395
0.862
Reflection
Resolution: 2.2→40 Å / Num. obs: 22288 / % possible obs: 99.3 % / Rmerge(I) obs: 0.11 / Χ2: 1.029 / Net I/σ(I): 15.353
Reflection shell
Resolution (Å)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
2.2-2.28
0.395
2186
0.862
98.6
2.28-2.37
0.373
2207
0.842
99.9
2.37-2.48
0.31
2203
0.81
100
2.48-2.61
0.273
2236
0.858
99.9
2.61-2.77
0.227
2209
0.952
99.9
2.77-2.99
0.176
2233
0.937
100
2.99-3.29
0.138
2232
1.078
99.8
3.29-3.76
0.103
2248
1.086
99.8
3.76-4.74
0.086
2262
1.39
99
4.74-40
0.069
2272
1.285
96.1
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
refinement
PDB_EXTRACT
3.006
dataextraction
Refinement
Resolution: 2.2→14.73 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.822 / SU B: 6.084 / SU ML: 0.155 / SU R Cruickshank DPI: 0.243 / SU Rfree: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH Y164 MUTATED TO A G IN THE FIRST OF THE TWO HALVES. BECAUSE THE CRYSTAL IS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH Y164 MUTATED TO A G IN THE FIRST OF THE TWO HALVES. BECAUSE THE CRYSTAL IS ISOMORPHOUS WITH WTUROD IN WHICH THERE IS A MONOMER IN THE ASYMMETRIC UNIT, THE AUTHORS HAVE MODELED Y164 AT ONE-HALF OCCUPANCY. THIS ACCOUNTS FOR THE STOCHASTIC ARRANGEMENT OF THE FUSION DIMER IN THE CRYSTAL SUCH THAT RESIDUE 164 IS EFFECTIVELY HALF Y AND HALF G.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.246
1145
5.1 %
RANDOM
Rwork
0.194
-
-
-
obs
0.197
22265
99.08 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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