4RE5

Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HU5PDB entry 2HU5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529378 mM sodium acetate buffer, 2.4% w/v PEG Mw4000, 6.7mM dithiothreitol and 0.44 mM EDTA. The protein was co-crystallized with the inhibitor., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2445.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.813α = 90
b = 104.43β = 90
c = 170.08γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors (Blue)2010-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.92099.70.06217.583.939002290022-332.79
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)
11.91.9599.90.6822.273.81

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2HU51.919.938552085520449999.660.179020.179020.176950.2181RANDOM, imported from isostructural data set of pdb entry 2HU535.253
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]
-0.31-1.371.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.581
r_dihedral_angle_4_deg18.933
r_dihedral_angle_3_deg13.426
r_long_range_B_refined7.089
r_long_range_B_other7.089
r_dihedral_angle_1_deg6.303
r_scangle_other3.994
r_mcangle_it2.735
r_mcangle_other2.735
r_scbond_it2.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.581
r_dihedral_angle_4_deg18.933
r_dihedral_angle_3_deg13.426
r_long_range_B_refined7.089
r_long_range_B_other7.089
r_dihedral_angle_1_deg6.303
r_scangle_other3.994
r_mcangle_it2.735
r_mcangle_other2.735
r_scbond_it2.68
r_scbond_other2.679
r_mcbond_it1.876
r_mcbond_other1.876
r_angle_refined_deg1.72
r_angle_other_deg1.14
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8591
Nucleic Acid Atoms
Solvent Atoms662
Heterogen Atoms69

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling