4JBS

Crystal structure of the human Endoplasmic Reticulum Aminopeptidase 2 in complex with PHOSPHINIC PSEUDOTRIPEPTIDE inhibitor.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E36PDB ENTRY 4E36

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.528910% PEG 8000, 20% ethylene glycol, 69 mM MES, 31 mM imidazole.Drops incubated at 277 K before being transferred to 289 K, pH 6.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.9257.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.15α = 90
b = 134.77β = 90.28
c = 128.731γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.7894994.810.0653.2125739119216-5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.792.9499.90.283.4

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4E362.78910.9940.62123709117190629494.730.210.20640.2778
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]
4.00676.9545-6.93972.1171
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.319
f_angle_d0.872
f_chiral_restr0.058
f_bond_d0.008
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13862
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms288

Software

Software
Software NamePurpose
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling