- PDB-5mdo: Crystal structure of in vitro folded Chitoporin VhChip from Vibri... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5mdo
Title
Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal form I)
Components
Chitoporin
Keywords
SUGAR BINDING PROTEIN / outer membrane protein / Vibrio harveyi / Chitin / porin
Function / homology
Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin domain superfamily / porin activity / monoatomic ion transmembrane transport / cell outer membrane / metal ion binding / Chitoporin
Function and homology information
Biological species
Vibrio harveyi (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97949 Å / Relative weight: 1
Reflection
Resolution: 1.95→64.97 Å / Num. obs: 336423 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.046 / Net I/σ(I): 13.9
Reflection shell
Resolution: 1.95→1.98 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.854 / Rpim(I) all: 0.543 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0131
refinement
XDS
datareduction
Aimless
datascaling
AutoSol
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.95→129.94 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.129 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1867
3124
0.9 %
RANDOM
Rwork
0.16708
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obs
0.16726
333266
99.95 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å