3O4I

Structure and Catalysis of Acylaminoacyl Peptidase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529378mM sodium acetate, 0.44mM EDTA, 6.7mM dithiothreitol, 2.0% PEG 4000 , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.4472.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.63α = 90
b = 209.89β = 90
c = 205.92γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2008-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R0.9999ELETTRA5.2R

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
12.72099.30.09413.25.946153261532-3
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)
2.72.7799.80.5273.36.264545

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 REPLACEMENTTHROUGHOUTHydrolase and propeller domains of PDB entry 2HU5.2.719.85840758407309199.630.209340.209340.20710.25192RANDOM43.197
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]
0.18-0.1-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.464
r_dihedral_angle_4_deg21.663
r_dihedral_angle_3_deg16.576
r_dihedral_angle_1_deg6.414
r_scangle_it3.065
r_scbond_it1.938
r_angle_refined_deg1.734
r_angle_other_deg1.24
r_mcangle_it1.123
r_mcbond_it0.637
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.464
r_dihedral_angle_4_deg21.663
r_dihedral_angle_3_deg16.576
r_dihedral_angle_1_deg6.414
r_scangle_it3.065
r_scbond_it1.938
r_angle_refined_deg1.734
r_angle_other_deg1.24
r_mcangle_it1.123
r_mcbond_it0.637
r_mcbond_other0.267
r_chiral_restr0.097
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8568
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms37

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling