3O4J

Structure and Catalysis of Acylaminoacyl Peptidase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293170mM sodium acetate, 0.4mM EDTA, 10% dimethyl sulphoxide, 2.5% PEG 4000 , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.5272.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 184.27α = 90
b = 227.524β = 100.37
c = 110.684γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR555 FLAT PANELmirror2009-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8148EMBL/DESY, HAMBURGX11

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
12.53096.80.09211.433.3149375149375-3
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)
2.52.698.80.6422.483.316732

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 2HU5.2.529.52141856141856751996.890.200990.200990.199140.23589RANDOM35.233
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]
-0.02-0.020.11-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.229
r_dihedral_angle_4_deg19.254
r_dihedral_angle_3_deg15.887
r_dihedral_angle_1_deg6.245
r_scangle_it2.818
r_scbond_it1.855
r_angle_refined_deg1.748
r_angle_other_deg1.12
r_mcangle_it1.065
r_mcbond_it0.642
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.229
r_dihedral_angle_4_deg19.254
r_dihedral_angle_3_deg15.887
r_dihedral_angle_1_deg6.245
r_scangle_it2.818
r_scbond_it1.855
r_angle_refined_deg1.748
r_angle_other_deg1.12
r_mcangle_it1.065
r_mcbond_it0.642
r_mcbond_other0.354
r_chiral_restr0.097
r_bond_refined_d0.022
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.004
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 Atoms17452
Nucleic Acid Atoms
Solvent Atoms535
Heterogen Atoms33

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling