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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
3SY7
Improved crystal structure of Pseudomonas aeruginosa OprD
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
pH
5.5
Temperature
295.0
Details
2 M ammonium sulphate 50 mM Na-citrate, pH 5.5, VAPOR DIFFUSION, temperature 295K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 136.41
α = 90
b = 103.89
β = 107.68
c = 47.54
γ = 90
Symmetry
Space Group
C 1 2 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 315
--
2010-12-02
Diffraction Radiation
Monochromator
Protocol
Si(111)
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
NSLS BEAMLINE X25
1.10
NSLS
X25
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
2.15
50
98.0
--
--
--
--
34239
33554
0.0
2.7
--
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)
2.15
2.19
80.8
--
--
--
--
--
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
2.15
19.993
--
1.34
34239
33514
2001
97.55
--
0.1974
0.1956
0.2259
random
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
2.1488
2.2024
--
114
1768
0.2469
0.3244
--
77.0
X Ray Diffraction
2.2024
2.2619
--
138
2092
0.2469
0.2987
--
91.0
X Ray Diffraction
2.2619
2.3284
--
126
2260
0.2493
0.3447
--
98.0
X Ray Diffraction
2.3284
2.4034
--
151
2280
0.2114
0.2402
--
100.0
X Ray Diffraction
2.4034
2.4891
--
143
2325
0.1966
0.2542
--
100.0
X Ray Diffraction
2.4891
2.5886
--
156
2286
0.1835
0.2171
--
100.0
X Ray Diffraction
2.5886
2.7061
--
146
2310
0.1683
0.2129
--
100.0
X Ray Diffraction
2.7061
2.8484
--
142
2300
0.1829
0.2355
--
100.0
X Ray Diffraction
2.8484
3.0263
--
152
2302
0.1817
0.2399
--
100.0
X Ray Diffraction
3.0263
3.2591
--
147
2308
0.1746
0.205
--
100.0
X Ray Diffraction
3.2591
3.5853
--
146
2315
0.1831
0.2136
--
100.0
X Ray Diffraction
3.5853
4.1003
--
149
2305
0.1871
0.2072
--
100.0
X Ray Diffraction
4.1003
5.1512
--
149
2321
0.1764
0.1986
--
100.0
X Ray Diffraction
5.1512
19.9934
--
142
2341
0.2417
0.2405
--
99.0
Temperature Factor Modeling
Temperature Factor
Value
Anisotropic B[1][1]
4.3124
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
-0.9502
Anisotropic B[2][2]
-10.145
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
5.8326
RMS Deviations
Key
Refinement Restraint Deviation
f_chiral_restr
0.079
f_bond_d
0.007
f_dihedral_angle_d
19.873
f_plane_restr
0.004
f_angle_d
1.072
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2969
Nucleic Acid Atoms
0
Heterogen Atoms
78
Solvent Atoms
130
Software
Software
Software Name
Purpose
CBASS
data collection
PHASER
phasing
PHENIX
refinement version: (phenix.refine: 1.7.1_743)
HKL-2000
data reduction
HKL-2000
data scaling