3B2P

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72981.8 M Sodium malonate pH=7/0, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.4964.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.204α = 90
b = 120.204β = 90
c = 169.655γ = 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)2007-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0000ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
125099.90.10.0813.25.695605956052222.885
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0799.40.570.52.459360

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2HPO244.372029573692657285599.770.154480.153430.18846RANDOM20.646
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_deg36.97
r_dihedral_angle_4_deg18.644
r_dihedral_angle_3_deg14.035
r_dihedral_angle_1_deg6.017
r_scangle_it4.185
r_scbond_it2.53
r_angle_refined_deg1.434
r_mcangle_it1.393
r_mcbond_it0.731
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.97
r_dihedral_angle_4_deg18.644
r_dihedral_angle_3_deg14.035
r_dihedral_angle_1_deg6.017
r_scangle_it4.185
r_scbond_it2.53
r_angle_refined_deg1.434
r_mcangle_it1.393
r_mcbond_it0.731
r_nbtor_refined0.297
r_symmetry_vdw_refined0.239
r_symmetry_hbond_refined0.236
r_nbd_refined0.203
r_xyhbond_nbd_refined0.184
r_metal_ion_refined0.141
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6940
Nucleic Acid Atoms
Solvent Atoms765
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
APEXdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing