Mass: 34813.750 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-335 Source method: isolated from a genetically manipulated source Details: NAG LINKAGE AT N217 IN BOTH A, B CHAINS, FUC LINKAGE AT T311 IN A CHAIN Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK 293S / Production host: HOMO SAPIENS (human) / References: UniProt: P78504
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→30.19 Å / Cor.coef. Fo:Fc: 0.8933 / Cor.coef. Fo:Fc free: 0.8607 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.278 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.217 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4544. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4544. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.246
1596
5.05 %
RANDOM
Rwork
0.2176
-
-
-
obs
0.219
31595
96.97 %
-
Displacement parameters
Biso mean: 43.98 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.9395 Å2
-7.5398 Å2
-10.2841 Å2
2-
-
-3.3341 Å2
4.0638 Å2
3-
-
-
4.2736 Å2
Refine analyze
Luzzati coordinate error obs: 0.367 Å
Refinement step
Cycle: LAST / Resolution: 2.32→30.19 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4445
0
40
61
4546
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
4629
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.19
6286
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1575
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
133
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
679
HARMONIC
5
X-RAY DIFFRACTION
t_it
4629
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
0
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
3.59
X-RAY DIFFRACTION
t_other_torsion
18.02
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
570
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
4791
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.32→2.4 Å / Total num. of bins used: 16
Rfactor
Num. reflection
% reflection
Rfree
0.261
133
4.66 %
Rwork
0.2309
2724
-
all
0.2323
2857
-
obs
-
-
96.97 %
+
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