WDrepeat-containingprotein5 / BMP2-induced 3-kb gene protein
Mass: 34303.914 Da / Num. of mol.: 1 / Fragment: UNP residues 23-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BIG3, WDR5 / Plasmid: pHIS paralell / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: P61964
#2: Protein/peptide
Histone-lysineN-methyltransferaseMLL3 / Homologous to ALR protein / Lysine N-methyltransferase 2C / KMT2C / Myeloid/lymphoid or mixed- ...Homologous to ALR protein / Lysine N-methyltransferase 2C / KMT2C / Myeloid/lymphoid or mixed-lineage leukemia protein 3
Mass: 1478.693 Da / Num. of mol.: 1 / Fragment: UNP residues 4703-4716 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q8NEZ4, histone-lysine N-methyltransferase
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.917 Å / Relative weight: 1
Reflection
Redundancy: 12.3 % / Av σ(I) over netI: 58.92 / Number: 1028717 / Rmerge(I) obs: 0.081 / Χ2: 3.01 / D res high: 1.22 Å / D res low: 50 Å / Num. obs: 83725 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
3.31
50
96.2
1
0.063
5.741
12.8
2.63
3.31
100
1
0.054
3.042
14
2.3
2.63
100
1
0.062
2.956
14.1
2.09
2.3
100
1
0.074
3.503
14
1.94
2.09
100
1
0.085
3.649
13.8
1.82
1.94
100
1
0.101
3.656
13.5
1.73
1.82
100
1
0.125
3.5
13.3
1.66
1.73
100
1
0.146
3.323
13.1
1.59
1.66
100
1
0.169
3.222
12.9
1.54
1.59
100
1
0.196
3.039
12.8
1.49
1.54
100
1
0.228
2.83
12.7
1.45
1.49
100
1
0.259
2.691
12.5
1.41
1.45
100
1
0.304
2.499
12.5
1.37
1.41
100
1
0.349
2.35
12.4
1.34
1.37
100
1
0.401
2.229
12.3
1.31
1.34
100
1
0.454
2.164
12.2
1.29
1.31
99.9
1
0.503
2.102
11.8
1.26
1.29
100
1
0.561
2.058
10.4
1.24
1.26
99.5
1
0.582
1.98
8.2
1.22
1.24
96.9
1
0.634
1.846
6.3
Reflection
Resolution: 1.22→50 Å / Num. obs: 83725 / % possible obs: 99.6 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.081 / Χ2: 3.008 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.22-1.24
6.3
0.634
4003
1.846
1
96.9
1.24-1.26
8.2
0.582
4124
1.98
1
99.5
1.26-1.29
10.4
0.561
4147
2.058
1
100
1.29-1.31
11.8
0.503
4155
2.102
1
99.9
1.31-1.34
12.2
0.454
4166
2.164
1
100
1.34-1.37
12.3
0.401
4172
2.229
1
100
1.37-1.41
12.4
0.349
4130
2.35
1
100
1.41-1.45
12.5
0.304
4167
2.499
1
100
1.45-1.49
12.5
0.259
4175
2.691
1
100
1.49-1.54
12.7
0.228
4143
2.83
1
100
1.54-1.59
12.8
0.196
4208
3.039
1
100
1.59-1.66
12.9
0.169
4189
3.222
1
100
1.66-1.73
13.1
0.146
4168
3.323
1
100
1.73-1.82
13.3
0.125
4188
3.5
1
100
1.82-1.94
13.5
0.101
4210
3.656
1
100
1.94-2.09
13.8
0.085
4229
3.649
1
100
2.09-2.3
14
0.074
4232
3.503
1
100
2.3-2.63
14.1
0.062
4268
2.956
1
100
2.63-3.31
14
0.054
4315
3.042
1
100
3.31-50
12.8
0.063
4336
5.741
1
96.2
-
Phasing
Phasing
Method: molecular replacement
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
MOLREP
phasing
PHENIX
1.7.3_928
refinement
PDB_EXTRACT
3.11
dataextraction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→43.94 Å / Occupancy max: 1 / Occupancy min: 0.55 / FOM work R set: 0.8732 / SU ML: 0.19 / σ(F): 1.32 / Phase error: 19.41 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2091
3459
4.99 %
Rwork
0.1866
-
-
obs
0.1878
69347
99.67 %
Solvent computation
Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.962 Å2 / ksol: 0.386 e/Å3
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