3B37

Crystal structure of E. coli Aminopeptidase N in complex with Tyrosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HPO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72982M Sodium Malonate, pH=7.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.5164.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.324α = 90
b = 120.324β = 90
c = 170.345γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315KOHZU: Double Crystal Si(111)2007-01-25SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.75099.90.0432.245.315641115.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7699.30.442.94.315382

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2HPO1.749.88156281466299.880.1630.1620.184RANDOM14.593
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_deg36.515
r_dihedral_angle_4_deg18.879
r_dihedral_angle_3_deg12.27
r_dihedral_angle_1_deg5.578
r_scangle_it3.591
r_scbond_it2.115
r_angle_refined_deg1.207
r_mcangle_it1.177
r_mcbond_it0.593
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.515
r_dihedral_angle_4_deg18.879
r_dihedral_angle_3_deg12.27
r_dihedral_angle_1_deg5.578
r_scangle_it3.591
r_scbond_it2.115
r_angle_refined_deg1.207
r_mcangle_it1.177
r_mcbond_it0.593
r_nbtor_refined0.303
r_nbd_refined0.198
r_symmetry_vdw_refined0.194
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.143
r_metal_ion_refined0.122
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6940
Nucleic Acid Atoms
Solvent Atoms752
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing