2HPO

Structure of Aminopeptidase N from E. coli Suggests a Compartmentalized, Gated Active Site


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52981.8 M Sodium Malonate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.5265.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.438α = 90
b = 120.438β = 90
c = 170.561γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-11-14MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.9797, 0.9798, 0.9612ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.652095.50.5214.1164250164250
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6889.20.522.87598

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 DIFFRACTIONMADTHROUGHOUT1.6519.94164250141768433485.210.17850.157810.15710.18062RANDOM16.04
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]
-0.07-0.03-0.070.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.942
r_dihedral_angle_4_deg17.604
r_dihedral_angle_3_deg12.532
r_dihedral_angle_1_deg5.483
r_sphericity_free3.579
r_scangle_it3.025
r_sphericity_bonded2.574
r_scbond_it1.927
r_mcangle_it1.201
r_angle_refined_deg1.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.942
r_dihedral_angle_4_deg17.604
r_dihedral_angle_3_deg12.532
r_dihedral_angle_1_deg5.483
r_sphericity_free3.579
r_scangle_it3.025
r_sphericity_bonded2.574
r_scbond_it1.927
r_mcangle_it1.201
r_angle_refined_deg1.171
r_rigid_bond_restr1.098
r_mcbond_it0.779
r_nbtor_refined0.302
r_nbd_refined0.197
r_symmetry_vdw_refined0.182
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.151
r_chiral_restr0.082
r_metal_ion_refined0.037
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6940
Nucleic Acid Atoms
Solvent Atoms1162
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXSphasing