+
Open data
-
Basic information
Entry | Database: PDB / ID: 3v86 | ||||||
---|---|---|---|---|---|---|---|
Title | Computational Design of a Protein Crystal | ||||||
![]() | De novo design helix | ||||||
![]() | DE NOVO PROTEIN / Computational Design of a protein Crystal / Helical Coil / De novo designed helix | ||||||
Method | ![]() ![]() | ||||||
![]() | Acharya, R. / North, B. / Saven, J. / DeGrado, W. | ||||||
![]() | ![]() Title: Computational design of a protein crystal. Authors: Lanci, C.J. / Macdermaid, C.M. / Kang, S.G. / Acharya, R. / North, B. / Yang, X. / Qiu, X.J. / Degrado, W.F. / Saven, J.G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 13.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 427.7 KB | Display | |
Data in XML | ![]() | 3.2 KB | Display | |
Data in CIF | ![]() | 3.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dacC ![]() 1coiS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 3171.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized, De novo design protein |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.51 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10mg/ml peptide solution, well solution, 0.01M Cobalt(II) Chloride hexahydrate, 0.1M MES monohydrate pH 6.5, 1.8M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 13, 2005 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.505 |
Reflection | Resolution: 2.89→40.16 Å / Num. all: 741 / Num. obs: 711 / % possible obs: 95.95 % / Observed criterion σ(I): 3 / Redundancy: 8.5 % / Biso Wilson estimate: 51.38 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2.89→3.04 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 11.8 / Num. unique all: 86 / % possible all: 78 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: poly-alanine model generated from 1COI Resolution: 2.91→40 Å / Isotropic thermal model: 18.8 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 4 / Stereochemistry target values: Engh & Huber Details: REFINED TWIN FRACTION IS 0.505 AND TWIN LAW IS -H, -K, L, USED PROTOCOL IMPLEMENTED IN SHELXL
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.91→40 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.91→3.04 Å
|