3O4G

Structure and Catalysis of Acylaminoacyl Peptidase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529378mM sodium acetate, 0.44mM EDTA, 6.7mM DITHIOTHREITOL, 2.4% PEG 4000 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7855.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.212α = 89.01
b = 97.016β = 109.2
c = 109.494γ = 100.21
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirror2008-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X120.9786EMBL/DESY, HAMBURGX12

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
12.52094.10.08912.551.998867588675-3
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)
2.52.5694.90.5952.011.996634

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 2HU5.2.519.648423284232443994.380.217550.217550.21520.26166RANDOM37.533
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]
0.030.01-0.020.02-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.298
r_dihedral_angle_4_deg18.081
r_dihedral_angle_3_deg15.958
r_dihedral_angle_1_deg6.157
r_scangle_it1.472
r_angle_refined_deg1.218
r_scbond_it0.947
r_angle_other_deg0.861
r_mcangle_it0.538
r_mcbond_it0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.298
r_dihedral_angle_4_deg18.081
r_dihedral_angle_3_deg15.958
r_dihedral_angle_1_deg6.157
r_scangle_it1.472
r_angle_refined_deg1.218
r_scbond_it0.947
r_angle_other_deg0.861
r_mcangle_it0.538
r_mcbond_it0.316
r_mcbond_other0.138
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms17159
Nucleic Acid Atoms
Solvent Atoms340
Heterogen Atoms24

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling