2ZWS

Crystal Structure Analysis of neutral ceramidase from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPVAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.6453.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.175α = 90
b = 59.292β = 102.16
c = 70.976γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.45090.80.1020.102173.4131655131655-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4551.40.6210.6211.21.9

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 REPLACEMENTTHROUGHOUT1.422.6125017125017663090.670.175650.175650.174040.20641RANDOM20.951
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]
-0.03-0.030.06-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.976
r_dihedral_angle_4_deg16.067
r_dihedral_angle_3_deg14.405
r_dihedral_angle_1_deg10.331
r_sphericity_free5.079
r_rigid_bond_restr4.274
r_sphericity_bonded4.259
r_scangle_it4.119
r_scbond_it4.055
r_mcangle_it1.784
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.976
r_dihedral_angle_4_deg16.067
r_dihedral_angle_3_deg14.405
r_dihedral_angle_1_deg10.331
r_sphericity_free5.079
r_rigid_bond_restr4.274
r_sphericity_bonded4.259
r_scangle_it4.119
r_scbond_it4.055
r_mcangle_it1.784
r_angle_refined_deg1.652
r_mcbond_it1.207
r_nbtor_refined0.318
r_symmetry_vdw_refined0.24
r_nbd_refined0.229
r_chiral_restr0.153
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.146
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4897
Nucleic Acid Atoms
Solvent Atoms653
Heterogen Atoms131

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing