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139717
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
4LFC
Crystal Structure of 30S ribosomal subunit from Thermus thermophilus
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
Download Files
FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly (gz) (A)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Hanging Drop
pH
6.5
Temperature
277.0
Details
MPD, pH 6.5, hanging drop, temperature 277K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 401.83
α = 90
b = 401.83
β = 90
c = 175.89
γ = 90
Symmetry
Space Group
P 41 21 2
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 315
--
2010-11-07
Diffraction Radiation
Monochromator
Protocol
KOHZU HLD8-24
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
APS BEAMLINE 24-ID-C
0.98
APS
24-ID-C
Data Collection
Overall
Resolution (High)
Resolution (Low)
Percent Possible (Observed)
R Merge I (Observed)
R Sym I (Observed)
Net I Over Average Sigma (I)
Redundancy
Number Reflections (All)
Number Reflections (Observed)
Observed Criterion Sigma (F)
Observed Criterion Sigma (I)
B (Isotropic) From Wilson Plot
3.6
35
99.4
0.086
--
--
3.3
163923
163923
-3.0
-3.0
--
High Resolution Shell
Resolution (High)
Resolution (Low)
Percent Possible (All)
R Merge I (Observed)
R-Sym I (Observed)
Mean I Over Sigma (Observed)
Redundancy
Number Unique Reflections (All)
3.6
3.73
99.9
0.789
--
--
3.3
16240
Refinement
Statistics
Structure Solution Method
Refinement High Resolution
Refinement Low Resolution
Cut-off Sigma (I)
Cut-off Sigma (F)
Number of Reflections (All)
Number of Reflections (Observed)
Number of Reflections (R-Free)
Percent Reflections (Observed)
R-Factor (All)
R-Factor (Observed)
R-Work
R-Free
R-Free Selection Details
FOURIER SYNTHESIS
3.602
34.457
--
1.34
163849
163849
8182
99.36
0.1651
0.1651
0.1628
0.2089
FROM PDB ENTRY 2VQE
High Resolution Shell
Refinement method
Shell Resolution (High)
Shell Resolution (Low)
# of Reflections (Observed)
# of Reflections (R-Free)
# of Reflections (R-Work)
R-Factor (R-Work)
R-Factor (R-Free)
R-Factor (R-Free Error)
Percent Reflections (Observed)
X Ray Diffraction
3.602
3.6429
--
251
5127
0.2824
0.329
--
100.0
X Ray Diffraction
3.6429
3.6857
--
296
5153
0.2558
0.2862
--
100.0
X Ray Diffraction
3.6857
3.7306
--
290
5110
0.2416
0.2983
--
100.0
X Ray Diffraction
3.7306
3.7778
--
295
5123
0.2362
0.2933
--
100.0
X Ray Diffraction
3.7778
3.8274
--
223
5238
0.2256
0.2891
--
100.0
X Ray Diffraction
3.8274
3.8798
--
264
5189
0.2047
0.2668
--
100.0
X Ray Diffraction
3.8798
3.9352
--
301
5105
0.1971
0.2368
--
100.0
X Ray Diffraction
3.9352
3.9938
--
251
5229
0.1888
0.2285
--
100.0
X Ray Diffraction
3.9938
4.0561
--
289
5131
0.1895
0.2379
--
100.0
X Ray Diffraction
4.0561
4.1225
--
296
5150
0.1722
0.2271
--
100.0
X Ray Diffraction
4.1225
4.1935
--
246
5183
0.164
0.2327
--
100.0
X Ray Diffraction
4.1935
4.2696
--
270
5166
0.1574
0.2162
--
100.0
X Ray Diffraction
4.2696
4.3516
--
287
5137
0.147
0.2026
--
100.0
X Ray Diffraction
4.3516
4.4402
--
271
5165
0.1435
0.1859
--
100.0
X Ray Diffraction
4.4402
4.5366
--
308
5141
0.1403
0.187
--
100.0
X Ray Diffraction
4.5366
4.6418
--
258
5203
0.1297
0.1719
--
100.0
X Ray Diffraction
4.6418
4.7576
--
248
5212
0.13
0.1836
--
100.0
X Ray Diffraction
4.7576
4.8859
--
260
5187
0.1319
0.1968
--
100.0
X Ray Diffraction
4.8859
5.0293
--
291
5200
0.1298
0.1889
--
100.0
X Ray Diffraction
5.0293
5.1911
--
258
5174
0.1228
0.1603
--
99.0
X Ray Diffraction
5.1911
5.376
--
262
5188
0.1223
0.1713
--
100.0
X Ray Diffraction
5.376
5.5903
--
283
5224
0.1239
0.18
--
100.0
X Ray Diffraction
5.5903
5.8436
--
278
5235
0.1246
0.1795
--
100.0
X Ray Diffraction
5.8436
6.15
--
249
5247
0.1272
0.1827
--
100.0
X Ray Diffraction
6.15
6.5329
--
264
5272
0.1292
0.1731
--
100.0
X Ray Diffraction
6.5329
7.0334
--
275
5246
0.1315
0.172
--
100.0
X Ray Diffraction
7.0334
7.7339
--
277
5247
0.136
0.178
--
99.0
X Ray Diffraction
7.7339
8.8365
--
277
5261
0.1482
0.2017
--
99.0
X Ray Diffraction
8.8365
11.0714
--
279
5248
0.1762
0.1989
--
98.0
X Ray Diffraction
11.0714
34.4583
--
285
5176
0.2335
0.2601
--
93.0
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
133.258
RMS Deviations
Key
Refinement Restraint Deviation
f_angle_d
1.425
f_dihedral_angle_d
17.259
f_chiral_restr
0.068
f_plane_restr
0.006
f_bond_d
0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
19153
Nucleic Acid Atoms
32504
Heterogen Atoms
183
Solvent Atoms
48
Software
Software
Software Name
Purpose
DENZO
data reduction
SCALEPACK
data scaling
PHENIX
refinement version: dev_1119
PDB_EXTRACT
data extraction version: 3.11
HKL-2000
data collection
PHENIX
phasing