3B34

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


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
3.5365.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.582α = 90
b = 120.582β = 90
c = 170.761γ = 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
11.35099.20.1238.28.93461712214.6
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)
11.31.3289.90.490.491.181.915484

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONTHROUGHOUT2HPO1.3504871113391831033397.160.1770.1770.19416Random18.757
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]
0.050.030.05-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.853
r_dihedral_angle_4_deg17.004
r_dihedral_angle_3_deg12.202
r_dihedral_angle_1_deg5.557
r_sphericity_bonded4.396
r_sphericity_free3.732
r_scangle_it3.342
r_scbond_it3.078
r_rigid_bond_restr3.061
r_mcangle_it1.356
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.853
r_dihedral_angle_4_deg17.004
r_dihedral_angle_3_deg12.202
r_dihedral_angle_1_deg5.557
r_sphericity_bonded4.396
r_sphericity_free3.732
r_scangle_it3.342
r_scbond_it3.078
r_rigid_bond_restr3.061
r_mcangle_it1.356
r_angle_refined_deg1.15
r_mcbond_it0.804
r_nbtor_refined0.296
r_nbd_refined0.197
r_symmetry_vdw_refined0.164
r_symmetry_hbond_refined0.149
r_metal_ion_refined0.14
r_xyhbond_nbd_refined0.131
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6940
Nucleic Acid Atoms
Solvent Atoms1113
Heterogen Atoms77

Software

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