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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
1PCV
Crystal structure of osmotin, a plant antifungal protein
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)
Biological Assembly 2 (gz) (A)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
8.5
Temperature
295.0
Details
lithium sulfate, nickel chloride, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 41.78
α = 100.84
b = 41.79
β = 92.41
c = 59.56
γ = 96.57
Symmetry
Space Group
P 1
Diffraction
Diffraction Radiation
Monochromator
Protocol
--
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
NSLS BEAMLINE X12C
1.100
NSLS
X12C
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
2.3
30
78.8
--
--
--
--
14549
13744
0.0
--
--
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
MOLECULAR REPLACEMENT
2.3
29.19
--
0.0
--
13744
688
78.8
--
--
0.211
0.257
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
2.3
2.44
1013
65
1013
0.24
0.256
0.032
36.8
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
RESTRAINED
Mean Isotropic B
21.0
Anisotropic B[1][1]
-0.82
Anisotropic B[1][2]
0.51
Anisotropic B[1][3]
5.84
Anisotropic B[2][2]
-4.29
Anisotropic B[2][3]
0.96
Anisotropic B[3][3]
5.11
RMS Deviations
Key
Refinement Restraint Deviation
c_improper_angle_d
0.92
c_scbond_it
1.66
c_mcangle_it
1.8
c_scangle_it
2.29
c_dihedral_angle_d
26.2
c_angle_deg
1.6
c_mcbond_it
1.14
c_bond_d
0.008
Coordinate Error
Parameter
Value
Luzzati ESD (Observed)
0.28
Luzzati Sigma A (Observed)
0.28
Luzzati Resolution Cutoff (Low)
5.0
Luzzati ESD (R-Free Set)
0.35
Luzzati Sigma A (R-Free Set)
0.24
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
3102
Nucleic Acid Atoms
0
Heterogen Atoms
0
Solvent Atoms
140
Software
Software
Software Name
Purpose
CNS
refinement version: 1.0
DENZO
data reduction
SCALEPACK
data scaling
EPMR
phasing