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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
2CYG
Crystal structure at 1.45- resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome
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
Vapor Diffusion Hanging Drop
pH
4.6
Temperature
293.0
Details
Sodium formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 48.27
α = 90
b = 53.93
β = 90
c = 113.55
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
CCD
ADSC QUANTUM 4
--
2002-12-04
Diffraction Radiation
Monochromator
Protocol
single wavelength
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
ESRF BEAMLINE ID14-2
0.933
ESRF
ID14-2
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
1.45
20
97.7
0.035
0.035
--
3.6
53238
52014
0.0
0.0
10.46
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)
1.45
1.5
97.7
0.129
0.129
5.6
3.6
4819
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
1.45
20.0
0.0
0.0
52014
49317
2644
97.4
0.15835
0.15835
0.15722
0.1794
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
1.45
1.487
3416
194
3416
0.16
0.189
--
0.05
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
14.92
RMS Deviations
Key
Refinement Restraint Deviation
r_symmetry_vdw_other
0.188
r_chiral_restr
0.067
r_symmetry_vdw_refined
0.097
r_gen_planes_refined
0.004
r_nbd_other
0.229
r_angle_refined_deg
1.095
r_xyhbond_nbd_refined
0.118
r_symmetry_hbond_refined
0.124
r_mcbond_it
0.384
r_scbond_it
1.206
r_mcangle_it
0.761
r_scangle_it
1.938
r_bond_refined_d
0.006
r_nbd_refined
0.195
r_angle_other_deg
0.787
r_gen_planes_other
0.001
r_nbtor_other
0.078
r_dihedral_angle_1_deg
6.01
r_bond_other_d
0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2395
Nucleic Acid Atoms
0
Heterogen Atoms
0
Solvent Atoms
407
Software
Software
Software Name
Purpose
REFMAC
refinement version: 5.1.19
DENZO
data reduction
CCP4
data scaling version: (SCALA)
AMoRE
phasing