- PDB-2vnm: Human BACE-1 in complex with 3-(1,1-dioxidotetrahydro-2H-1,2-thia... -
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Open data
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Basic information
Entry
Database: PDB / ID: 2vnm
Title
Human BACE-1 in complex with 3-(1,1-dioxidotetrahydro-2H-1,2-thiazin- 2-yl)-5-(ethylamino)-N-((1S,2R)-2-hydroxy-1-(phenylmethyl)-3-(((3-(trifluoromethyl)phenyl)methyl)amino)propyl)benzamide
SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.
Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Compound details
ENGINEERED RESIDUE IN CHAIN A, ASN 153 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 172 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, ASN 153 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 172 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 223 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASN 354 TO GLN
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 1.98 Å3/Da / Density % sol: 43.59 % / Description: NONE
Crystal grow
Temperature: 293 K / Method: vapor diffusion Details: CRYSTALS GROWN BY VAPOUR DIFFUSION AT 20C USING STREAK SEEDING, WITH 10% PEG8000 AND 0.1M GLYCINE PH 3.2
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0723 Å / Relative weight: 1
Reflection
Resolution: 1.79→40 Å / Num. obs: 201388 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.7
Reflection shell
Resolution: 1.79→1.82 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7
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Processing
Software
Name
Version
Classification
REFMAC
5.3.0006
refinement
DENZO
datareduction
SCALEPACK
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 1.79→61.55 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.623 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TWO MOLECULES OF THE LIGAND SEEN IN THIS STRUCTURE, ONE IN THE ACTIVE SITE AND ONE BETWEEN CRYSTAL CONTACTS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.231
1469
4 %
RANDOM
Rwork
0.191
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obs
0.192
35018
99.1 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK