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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
4FCZ
Crystal Structure of Toluene-tolerance protein from Pseudomonas putida (strain KT2440), Northeast Structural Genomics Consortium (NESG) Target PpR99
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 1 (gz) (A+S)
Biological Assembly 2 (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
7.5
Details
Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 79.87
α = 90
b = 40.88
β = 106.49
c = 82.4
γ = 90
Symmetry
Space Group
P 1 21 1
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
MAR CCD 165 mm
mirrors
2011-04-14
Diffraction Radiation
Monochromator
Protocol
Si 111 CHANNEL
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
NSLS BEAMLINE X4C
0.979
NSLS
X4C
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
2.6
39.09
94.7
0.112
--
--
5.4
--
28693
--
-3.0
--
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
SAD
2.604
39.086
--
0.13
--
14803
1574
92.3
--
0.2367
0.2326
0.2976
--
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
2.6067
2.6908
--
92
817
0.2827
0.3678
--
56.0
X Ray Diffraction
2.6908
2.7869
--
121
1034
0.2723
0.3707
--
72.0
X Ray Diffraction
2.7869
2.8984
--
127
1184
0.2611
0.3219
--
82.0
X Ray Diffraction
2.8984
3.0303
--
134
1200
0.2645
0.3526
--
85.0
X Ray Diffraction
3.0303
3.1899
--
144
1249
0.2569
0.2924
--
86.0
X Ray Diffraction
3.1899
3.3896
--
140
1280
0.2377
0.3164
--
88.0
X Ray Diffraction
3.3896
3.6511
--
152
1262
0.2325
0.3015
--
88.0
X Ray Diffraction
3.6511
4.018
--
146
1293
0.2112
0.281
--
89.0
X Ray Diffraction
4.018
4.5983
--
144
1305
0.2062
0.2267
--
89.0
X Ray Diffraction
4.5983
5.789
--
150
1311
0.2134
0.287
--
89.0
X Ray Diffraction
5.789
34.6058
--
152
1359
0.2188
0.3069
--
89.0
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
43.825
Anisotropic B[1][1]
-7.206
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
-6.274
Anisotropic B[2][2]
1.742
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
5.464
RMS Deviations
Key
Refinement Restraint Deviation
f_bond_d
0.009
f_dihedral_angle_d
16.232
f_plane_restr
0.006
f_chiral_restr
0.076
f_angle_d
1.189
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2862
Nucleic Acid Atoms
0
Heterogen Atoms
0
Solvent Atoms
41
Software
Software
Software Name
Purpose
PHENIX
refinement version: dev_1269
PDB_EXTRACT
data extraction version: 3.100
ADSC
data collection version: Quantum
HKL-2000
data reduction
SCALEPACK
data scaling
PHENIX
phasing version: (AutoSolve)