4XNB

Crystal Structure of E. coli Aminopeptidase N in complex with L-Beta Homophenylalanine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298Sodium malonate
Crystal Properties
Matthews coefficientSolvent content
3.5865.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.191α = 90
b = 120.191β = 90
c = 169.921γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2014-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
11.952099.90.1120.238.3103333
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0299.63.468.3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2HPO1.9519.1697810514199.410.133830.132180.16476RANDOM24.262
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_deg37.328
r_dihedral_angle_4_deg17.755
r_dihedral_angle_3_deg12.538
r_long_range_B_refined7.885
r_long_range_B_other7.506
r_dihedral_angle_1_deg6.142
r_scangle_other5.637
r_scbond_it3.867
r_scbond_other3.862
r_mcangle_it2.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.328
r_dihedral_angle_4_deg17.755
r_dihedral_angle_3_deg12.538
r_long_range_B_refined7.885
r_long_range_B_other7.506
r_dihedral_angle_1_deg6.142
r_scangle_other5.637
r_scbond_it3.867
r_scbond_other3.862
r_mcangle_it2.52
r_mcangle_other2.52
r_angle_refined_deg2.016
r_mcbond_it1.969
r_mcbond_other1.969
r_angle_other_deg1.091
r_chiral_restr0.135
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6940
Nucleic Acid Atoms
Solvent Atoms1061
Heterogen Atoms182

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing