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Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
3TGT
Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 gp120 core
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+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
7.5
Temperature
293.0
Details
14% PEG 1500, 12% PEG 400, 0.1M HEPES, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 63.56
α = 90
b = 66.94
β = 90
c = 88.03
γ = 90
Symmetry
Space Group
P 21 21 21
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
IMAGE PLATE
MAR scanner 300 mm plate
--
2010-07-16
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
APS BEAMLINE 22-BM
1
APS
22-BM
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
1.9
50
95.2
0.084
0.074
--
6.8
32465
30907
0.0
0.0
--
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)
1.9
1.93
86.5
0.615
0.555
2.1
5.5
--
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
MOLECULAR REPLACEMENT
1.9
24.571
--
0.11
31824
29250
1437
91.91
--
0.191
0.189
0.2307
--
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
1.8676
1.9343
--
83
1817
0.2349
0.2307
--
61.0
X Ray Diffraction
1.9343
2.0117
--
152
2475
0.2176
0.276
--
84.0
X Ray Diffraction
2.0117
2.1032
--
166
2717
0.2093
0.313
--
92.0
X Ray Diffraction
2.1032
2.214
--
144
2814
0.2029
0.261
--
94.0
X Ray Diffraction
2.214
2.3526
--
141
2858
0.197
0.256
--
95.0
X Ray Diffraction
2.3526
2.5341
--
158
2896
0.2037
0.244
--
97.0
X Ray Diffraction
2.5341
2.7888
--
152
2953
0.1966
0.2692
--
98.0
X Ray Diffraction
2.7888
3.1916
--
142
3038
0.1973
0.2095
--
99.0
X Ray Diffraction
3.1916
4.0182
--
145
3055
0.1776
0.2326
--
99.0
X Ray Diffraction
4.0182
24.5735
--
154
3190
0.1747
0.1972
--
99.0
Temperature Factor Modeling
Temperature Factor
Value
Anisotropic B[1][1]
10.722
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
-4.9969
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-5.7251
RMS Deviations
Key
Refinement Restraint Deviation
f_bond_d
0.007
f_chiral_restr
0.069
f_dihedral_angle_d
15.937
f_plane_restr
0.004
f_angle_d
1.198
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2677
Nucleic Acid Atoms
0
Heterogen Atoms
155
Solvent Atoms
148
Software
Software
Software Name
Purpose
PHENIX
refinement version: 1.6.1_357
PDB_EXTRACT
data extraction version: 3.10
DENZO
data reduction
SCALEPACK
data scaling