Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
Y
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Selenomethionine-derivatised PotE at 10 mg/mL in 50 mM sodium chloride, 5 mM Tris-HCl pH 8.0 was crystallised from 20% (w/v) PEG 1,000, 100 mM Tris-HCl pH 8.5
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source
Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97919 Å
Method to determine structure: SAD / Resolution: 2→37.13 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.194 / SU Rfree Blow DPI: 0.177 / SU Rfree Cruickshank DPI: 0.178
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.251
658
4.79 %
RANDOM
Rwork
0.193
-
-
-
obs
0.196
13728
99.1 %
-
Displacement parameters
Biso mean: 33.96 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.8094 Å2
0 Å2
-0.5181 Å2
2-
-
-2.1767 Å2
0 Å2
3-
-
-
-0.6327 Å2
Refine analyze
Luzzati coordinate error obs: 0.27 Å
Refinement step
Cycle: 1 / Resolution: 2→37.13 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1605
0
12
107
1724
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
1657
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.07
2236
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
758
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
42
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
228
HARMONIC
5
X-RAY DIFFRACTION
t_it
1657
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
4.25
X-RAY DIFFRACTION
t_other_torsion
2.76
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
207
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
1894
SEMIHARMONIC
4
LS refinement shell
Resolution: 2→2.16 Å / Total num. of bins used: 7
Rfactor
Num. reflection
% reflection
Rfree
0.3131
104
3.67 %
Rwork
0.222
2733
-
all
0.2252
2837
-
obs
-
-
99.27 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
3.7829
0.1477
-0.8994
1.0841
0.6255
1.8268
-0.059
-0.1425
-0.2468
0.0528
-0.0044
0.0039
0.1238
-0.0041
0.0633
-0.0229
0.0148
-0.0514
-0.0256
0.0353
0.0585
11.1743
27.0244
45.3082
2
2.7653
0.3776
0.2172
1.3834
-0.3952
1.1026
0.1177
-0.1069
0.1518
0.0697
-0.0519
0.0461
-0.0694
-0.0346
-0.0658
-0.0249
0.0028
-0.0347
-0.038
-0.0208
0.0512
9.4251
40.1636
25.528
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{A|31 - 127}
2
X-RAY DIFFRACTION
2
{B|31 - 127}
+
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