2HU8

Binding of inhibitors by Acylaminoacyl peptidase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829320mM Tris/HCl, 20% ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.81α = 90
b = 103.922β = 90
c = 169.255γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IIC2005-10-21MSINGLE 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
12.419.9699.10.13711.6845009-3
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)
12.42.599.90.384.465151

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.419.964295442954226499.560.217780.217780.21550.26128RANDOM (as for related pdb entry 2HU5)5.952
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]
-0.25-0.170.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.791
r_angle_other_deg0.887
r_angle_refined_deg0.878
r_scangle_it0.414
r_scbond_it0.264
r_symmetry_vdw_refined0.256
r_symmetry_hbond_refined0.251
r_nbd_other0.242
r_symmetry_vdw_other0.231
r_xyhbond_nbd_refined0.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.791
r_angle_other_deg0.887
r_angle_refined_deg0.878
r_scangle_it0.414
r_scbond_it0.264
r_symmetry_vdw_refined0.256
r_symmetry_hbond_refined0.251
r_nbd_other0.242
r_symmetry_vdw_other0.231
r_xyhbond_nbd_refined0.195
r_nbd_refined0.185
r_mcangle_it0.109
r_nbtor_other0.084
r_mcbond_it0.061
r_chiral_restr0.055
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8584
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing