Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.979156
1
3
0.979535
1
Reflection
Resolution: 1.55→29.3 Å / Num. obs: 32369 / % possible obs: 76.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 5.9
Reflection shell
Diffraction-ID: 1
Resolution (Å)
% possible obs (%)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Rsym value
% possible all
1.55-1.63
30.6
2.1
0.406
1.3
1836
0.406
30.6
1.63-1.73
45.8
2.5
0.28
2.7
2612
0.28
1.73-1.85
64.3
3
0.205
3.6
3466
0.205
1.85-2
93.2
3.5
0.15
4.6
4675
0.15
2-2.19
99.8
3.7
0.108
6.2
4663
0.108
2.19-2.45
99.8
3.7
0.088
7.3
4219
0.088
2.45-2.83
99.7
3.7
0.078
7.9
3748
0.078
2.83-3.47
99.5
3.7
0.059
9.8
3193
0.059
3.47-4.9
99.5
3.6
0.056
9.6
2524
0.056
4.9-29.29
97.8
3.4
0.065
6.9
1433
0.065
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
SCALA
datascaling
PDB_EXTRACT
1.601
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.55→29.3 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.569 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THE NOMINAL RESOLUTION IS 1.70 A WITH 3511 OBSERVED REFLECTIONS BETWEEN 1.70-1.55 (34.9% COMPLETE FOR THIS SHELL) INCLUDED IN THE ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THE NOMINAL RESOLUTION IS 1.70 A WITH 3511 OBSERVED REFLECTIONS BETWEEN 1.70-1.55 (34.9% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT. (3) TLSMD WAS USED TO EVALUATE TLS GROUPINGS. (4) K+ AND CL- IONS WERE MODELED BASED ON DENSITY HEIGHT, COORDINATION, ENVIRONMENT AND CRYSTALLIZATION CONDITIONS. (5) THERE IS SOME DIFFERENCE DENSITY NEAR GLU-40 THAT WAS LEFT UNMODELED. THE HOMOLOGOUS SITE IN 1E1A IS A LOW AFINITY CA2+ BINDING SITE. THE DENSITY DOES NOT LOOK LIKE CA2+ IN THIS STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.176
1606
5 %
RANDOM
Rwork
0.137
-
-
-
all
0.139
-
-
-
obs
0.13911
30729
76.58 %
-
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: 11.803 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.92 Å2
0 Å2
0 Å2
2-
-
0.01 Å2
0 Å2
3-
-
-
-0.93 Å2
Refinement step
Cycle: LAST / Resolution: 1.55→29.3 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2229
0
6
378
2613
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
2332
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2128
X-RAY DIFFRACTION
r_angle_refined_deg
1.528
1.959
3180
X-RAY DIFFRACTION
r_angle_other_deg
0.81
3
4938
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.168
5
310
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.808
23.232
99
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.549
15
369
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.506
15
17
X-RAY DIFFRACTION
r_chiral_restr
0.097
0.2
355
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
2656
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
484
X-RAY DIFFRACTION
r_nbd_refined
0.207
0.2
361
X-RAY DIFFRACTION
r_nbd_other
0.192
0.2
2123
X-RAY DIFFRACTION
r_nbtor_refined
0.169
0.2
1140
X-RAY DIFFRACTION
r_nbtor_other
0.083
0.2
1435
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.151
0.2
231
X-RAY DIFFRACTION
r_metal_ion_refined
0.107
0.2
4
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.068
0.2
5
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.25
0.2
42
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.154
0.2
23
X-RAY DIFFRACTION
r_mcbond_it
1.684
3
1480
X-RAY DIFFRACTION
r_mcbond_other
0.524
3
614
X-RAY DIFFRACTION
r_mcangle_it
2.701
5
2381
X-RAY DIFFRACTION
r_scbond_it
4.138
8
857
X-RAY DIFFRACTION
r_scangle_it
6.241
11
791
LS refinement shell
Resolution: 1.55→1.591 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.258
42
-
Rwork
0.223
784
-
obs
-
-
26.68 %
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
9.12
-1.7706
4.9117
2.795
-0.3241
5.3446
0.1602
0.1087
-0.0755
-0.0338
-0.0748
0.0029
0.5045
-0.0651
-0.0854
0.0484
0.0143
0.0298
0.0016
-0.0026
-0.0133
9.435
27.777
-7.397
2
0.134
0.2173
0.1624
1.4117
-0.1949
1.7559
-0.0074
0.0073
-0.0094
0.0021
-0.0261
-0.1599
0.1372
0.2176
0.0334
-0.0121
0.009
0.0022
0.0555
0.0194
0.0246
19.814
38.743
12.746
3
0.4484
-0.0004
0.2706
0.4628
-0.3687
1.6105
-0.0243
-0.0831
0.0418
0.0882
-0.0005
0.0335
-0.1118
-0.1358
0.0249
0.0057
0.012
0.0059
0.0262
0.001
0.0067
7.157
48.255
16.944
4
0.4269
-0.0839
0.127
1.0624
0.0913
1.2418
0.0055
-0.0019
-0.0066
-0.1381
-0.0559
0.0607
-0.0375
-0.1914
0.0503
-0.0172
0.0112
-0.005
0.0364
-0.0009
-0.0024
0.882
43.323
0.195
5
2.6373
1.835
-1.0237
2.6797
-0.2524
3.4441
0.0379
0.0835
0.0417
-0.126
0.0674
-0.0364
0.1191
0.0857
-0.1052
0.0058
0.0234
0.0022
0.0325
0.0184
0.0384
14.116
36.303
-0.544
6
0.8486
0.3033
0.6847
1.4553
0.3686
2.495
0.1042
-0.0797
-0.1065
-0.0293
-0.0504
0.0613
0.3619
-0.1144
-0.0539
0.0287
-0.0073
0.0136
0.0423
0.0218
0.0297
12.224
32.729
4.769
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: all / Auth asym-ID: A / Label asym-ID: A
ID
Refine TLS-ID
Auth seq-ID
Label seq-ID
1
1
20 - 30
32 - 42
2
2
31 - 103
43 - 115
3
3
104 - 168
116 - 180
4
4
169 - 258
181 - 270
5
5
259 - 273
271 - 285
6
6
274 - 314
286 - 326
+
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