4OID

Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NJQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1829530% PEG400, 0.1M Tris, 0.2M MgCl2, 0.1mM ZnCl2 , pH 8.0, Microbatch Crystallization, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.9558.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.606α = 90
b = 133.606β = 90
c = 320.959γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4APAL/PLS4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.35086946822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.598.53.5

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 (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4NJQ2.331.88467888578467898.490.159690.157180.160.206840.21RANDOM26.86
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.514
r_dihedral_angle_4_deg16.586
r_dihedral_angle_3_deg15.947
r_dihedral_angle_1_deg8.021
r_angle_refined_deg2.011
r_angle_other_deg1.105
r_chiral_restr0.135
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12609
Nucleic Acid Atoms
Solvent Atoms619
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing