4MVK

Crystal structure of an engineered lipocalin (Anticalin US7) in complex with the Alzheimer amyloid peptide fragment VFFAED


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L6MPDB ENTRY 1L6M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529327 % (w/v) PEG 8000, 100 mM MES, pH 6.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.97α = 90
b = 59.23β = 90
c = 61.23γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2010-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.542.57199.80.07813.27.130318303182
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.581000.3480.348274357

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1L6M1.542.573031830226153099.60.16640.16540.16540.1857RANDOM24.3619
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.6-0.26-1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.71
r_dihedral_angle_4_deg18.517
r_dihedral_angle_3_deg14.337
r_dihedral_angle_1_deg8.078
r_angle_refined_deg2.104
r_chiral_restr0.178
r_bond_refined_d0.023
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1441
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection