Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.1 Å3/Da / Density % sol: 41 % Description: SAD DATA WERE COLLECTED IN SITU IN CHIPX DEVICE AT ROOM TEMPERATURE.
Crystal grow
Temperature: 293 K / Method: counter-diffusion / pH: 4.5 Details: LYSOZYME WAS CRYSTALLIZED AT 293 K BY COUNTER-DIFFUSION IN A CHIPX MICROFLUIDIC DEVICE. MICROFLUIDIC CHANNELS WERE FILLED WITH A 50 MG/ML LYSOZYME SOLUTION CONTAINING 0.3% BETA-OCTYL- ...Details: LYSOZYME WAS CRYSTALLIZED AT 293 K BY COUNTER-DIFFUSION IN A CHIPX MICROFLUIDIC DEVICE. MICROFLUIDIC CHANNELS WERE FILLED WITH A 50 MG/ML LYSOZYME SOLUTION CONTAINING 0.3% BETA-OCTYL-GLUCOSIDE (M/V) TO FACILITATE SAMPLE LOADING BY CAPILLARITY. CRYSTALLANT RESERVOIRS WERE FILLED WITH 1.8 M NACL, 0.1 M SODIUM ACETATE PH 4.5 AND 0.05 M HPDO3A-YB.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.38 Å / Relative weight: 1
Reflection
Resolution: 1.7→30 Å / Num. obs: 21245 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 29.35 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shell
Resolution: 1.7→1.85 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.3 / % possible all: 93.9
-
Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
XSCALE
datascaling
SHELX
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 1.701→27.966 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 20.64 / Stereochemistry target values: ML Details: STRUCTURE DETERMINED BY SAD PHASING WITH DATA COLLECTED ON-CHIP AT ROOM TEMPERATURE. THE HPDO3A LIGAND OF YB IS NOT CLEARLY DEFINED IN THE DENSITY AND IS NOT INCLUDED IN THE MODEL.
Rfactor
Num. reflection
% reflection
Rfree
0.1925
1156
5 %
Rwork
0.1862
-
-
obs
0.1865
23130
90.3 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 30.73 Å2
Refinement step
Cycle: LAST / Resolution: 1.701→27.966 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1001
0
2
55
1058
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.006
1025
X-RAY DIFFRACTION
f_angle_d
1.093
1381
X-RAY DIFFRACTION
f_dihedral_angle_d
11.489
365
X-RAY DIFFRACTION
f_chiral_restr
0.087
144
X-RAY DIFFRACTION
f_plane_restr
0.003
181
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.7007-1.7781
0.3098
144
0.2436
2779
X-RAY DIFFRACTION
91
1.7781-1.8718
0.2698
144
0.2146
2840
X-RAY DIFFRACTION
93
1.8718-1.9891
0.2418
148
0.194
2773
X-RAY DIFFRACTION
91
1.9891-2.1426
0.2075
149
0.1807
2801
X-RAY DIFFRACTION
92
2.1426-2.3581
0.1921
146
0.1754
2756
X-RAY DIFFRACTION
92
2.3581-2.6991
0.245
142
0.1926
2699
X-RAY DIFFRACTION
89
2.6991-3.3996
0.1704
142
0.2049
2674
X-RAY DIFFRACTION
88
3.3996-27.9698
0.1683
141
0.1705
2652
X-RAY DIFFRACTION
87
+
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