4XND

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


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
3.6566.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.12α = 90
b = 121.12β = 90
c = 170.781γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-01-01MSINGLE 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
11.932099.50.09517.975.8108172
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.93298.63.25.5

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 REPLACEMENTTHROUGHOUT2HPO1.9320102499538499.050.135070.133420.16612RANDOM24.599
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.099
r_dihedral_angle_4_deg18.553
r_dihedral_angle_3_deg13.45
r_long_range_B_refined8.498
r_long_range_B_other8.169
r_scangle_other6.236
r_dihedral_angle_1_deg6.136
r_scbond_other4.234
r_scbond_it4.233
r_mcangle_it2.612
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.099
r_dihedral_angle_4_deg18.553
r_dihedral_angle_3_deg13.45
r_long_range_B_refined8.498
r_long_range_B_other8.169
r_scangle_other6.236
r_dihedral_angle_1_deg6.136
r_scbond_other4.234
r_scbond_it4.233
r_mcangle_it2.612
r_mcangle_other2.611
r_mcbond_it2.055
r_mcbond_other2.054
r_angle_refined_deg2
r_angle_other_deg1.072
r_chiral_restr0.129
r_bond_refined_d0.021
r_gen_planes_refined0.012
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 Atoms865
Heterogen Atoms255

Software

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