BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0), FOLLOWED BY THE TARGET SEQUENCE.
Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
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Sample preparation
Crystal
ID
Density Matthews (Å3/Da)
Density % sol (%)
Description
1
3.53
65.12
TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. 2.47 ANGSTROM MAD DA TA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE THE STRUCTURE. THE RESOLUTION OF THE INITIAL MODEL WAS THEN EXTENDED USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRACTED TO 2.30 ANGSTROMS. THE CRYSTALS ARE TWINNED. THE STRUCTURE WAS P HASED WITHOUT DETWINNING THE DATA. THE DATA REDUCTIONS STATISTICS ARE PRIOR TO D ETWINNING. A TOTAL OF 130 REFLECTIONS COULD NOT BE DETWINNED BECAUSE THEIR TWIN- RELATED REFLECTIONS WERE NOT RECORDED.
2
TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. 2.47 ANGSTROM MAD DA TA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE THE STRUCTURE. THE RESOLUTION OF THE INITIAL MODEL WAS THEN EXTENDED USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRACTED TO 2.30 ANGSTROMS. THE CRYSTALS ARE TWINNED. THE STRUCTURE WAS P HASED WITHOUT DETWINNING THE DATA. THE DATA REDUCTIONS STATISTICS ARE PRIOR TO D ETWINNING. A TOTAL OF 130 REFLECTIONS COULD NOT BE DETWINNED BECAUSE THEIR TWIN- RELATED REFLECTIONS WERE NOT RECORDED.
Single, cylindricallybent, asymmetricallycutSi(220) crystal
SINGLEWAVELENGTH
M
x-ray
1
2
Doublecrystal
MAD
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1
1
2
0.97922
1
3
0.97939
1
4
0.91162
1
Reflection
Resolution: 2.3→28.273 Å / Num. obs: 18260 / % possible obs: 97.3 % / Redundancy: 3.66 % / Biso Wilson estimate: 46.09 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.61
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Diffraction-ID
% possible all
2.3-2.38
0.41
1.76
6212
1,2
92.9
2.38-2.48
0.337
2.1
7165
1,2
98.5
2.48-2.59
0.266
2.8
6684
1,2
98.2
2.59-2.73
0.232
3.6
6742
1,2
97.4
2.73-2.9
0.139
5.7
6781
1,2
98.2
2.9-3.12
0.095
8.4
6730
1,2
98.1
3.12-3.43
0.054
13.4
6623
1,2
97.5
3.43-3.93
0.039
20.4
6471
1,2
96.4
3.93-4.93
0.03
27.4
6566
1,2
98.2
4.93-28.3
0.021
30.1
6889
1,2
97.4
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
SOLVE
phasing
REFMAC
5.2.0019
refinement
XSCALE
datascaling
PDB_EXTRACT
2
dataextraction
ADSC
QUANTUM
datacollection
XDS
datareduction
Refinement
Method to determine structure: MAD / Resolution: 2.3→28.273 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.84 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. ANALYSIS OF THE DIFFRACTION DATA INDICATED HEMIHEDERAL TWINNING WITH A TWIN FRACTION ...Details: 1. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. ANALYSIS OF THE DIFFRACTION DATA INDICATED HEMIHEDERAL TWINNING WITH A TWIN FRACTION OF 0.135 AND WITH A TWIN LAW OF K,H,-L. 4. THE INITIAL REFINEMENT WAS AGAINST THE NON-DETWINNED DATA AND INCLUDED PHASE RESTRAINTS TO THE EXPERIMENTAL MAD PHASES FROM ANOTHER CRYSTAL. 5. FOR THE FINAL STAGES OF REFINEMENT, THE DIFFRACTION INTENSITIES WERE DETWINNED USING THE CCP4 PROGAM DETWIN WITH A TWIN FRACTION OF 0.135 AND A TWIN OPERATION OF K,H,-L. 6. ETHYLENE GLYCOL USED AS A CRYOPROTECTANT AND NITRATE FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 7. ELECTRON DENSITIES FOR MSE 1-THR 14 AND THR 263-GLN 269 WERE DISORDERED, THEREFORE THESE RESIDUES WERE NOT MODELED. 8. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 9. ASP 233 IS A RAMACHANDRAN OUTLIER EVEN THOUGH IT IS MODELED INTO WELL-ORDERED ELECTRON DENSITY. 10. UNEXPLAINED NEGATIVE DIFFERENCE ELECTRON DENSITY IS OBSERVED BETWEEN LEU 203 AND LEU 211.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.225
922
5.1 %
RANDOM
Rwork
0.173
-
-
-
all
0.175
-
-
-
obs
0.175
18113
98.39 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 60.7 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.08 Å2
0.04 Å2
0 Å2
2-
-
0.08 Å2
0 Å2
3-
-
-
-0.12 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→28.273 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1846
0
64
113
2023
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
1942
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1345
X-RAY DIFFRACTION
r_angle_refined_deg
1.449
2
2619
X-RAY DIFFRACTION
r_angle_other_deg
0.926
3
3287
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.053
5
251
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.576
23.768
69
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.499
15
308
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.875
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.076
0.2
311
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2112
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
355
X-RAY DIFFRACTION
r_nbd_refined
0.217
0.2
386
X-RAY DIFFRACTION
r_nbd_other
0.204
0.2
1543
X-RAY DIFFRACTION
r_nbtor_refined
0.174
0.2
953
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.2
1063
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.134
0.2
118
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.167
0.2
15
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.254
0.2
53
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.11
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
1.742
3
1281
X-RAY DIFFRACTION
r_mcbond_other
0.362
3
497
X-RAY DIFFRACTION
r_mcangle_it
2.897
5
2013
X-RAY DIFFRACTION
r_scbond_it
5.366
8
731
X-RAY DIFFRACTION
r_scangle_it
6.955
11
604
LS refinement shell
Resolution: 2.3→2.362 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.307
57
-
Rwork
0.252
1243
-
obs
-
1300
97.6 %
Refinement TLS params.
Method: refined / Origin x: 38.473 Å / Origin y: 32.615 Å / Origin z: 18.843 Å
11
12
13
21
22
23
31
32
33
T
-0.3324 Å2
-0.0486 Å2
-0.0338 Å2
-
-0.2195 Å2
0.0833 Å2
-
-
-0.2596 Å2
L
4.488 °2
-2.4518 °2
-0.9421 °2
-
3.0391 °2
0.6788 °2
-
-
1.4702 °2
S
-0.0573 Å °
-0.2827 Å °
-0.4242 Å °
-0.0967 Å °
0.1212 Å °
0.3692 Å °
0.2482 Å °
-0.1624 Å °
-0.0639 Å °
Refinement TLS group
Selection: ALL
+
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