3B2X

Crystal Structure of E. coli Aminopeptidase N in complex with Lysine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72982.0 M Sodium malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.5265.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.561α = 90
b = 120.561β = 90
c = 170.269γ = 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 8.2.21.0ALS8.2.2

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
11.55088.80.09213.45.320176022
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)
11.51.5548.60.5323.510919

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 REPLACEMENTTHROUGHOUTPDB entry 2HPO1.549.94201607604988.840.1470.1470.165RANDOM17.636
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]
-0.09-0.05-0.090.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.529
r_dihedral_angle_4_deg17.248
r_dihedral_angle_3_deg12.034
r_dihedral_angle_1_deg5.427
r_scangle_it3.439
r_scbond_it2.182
r_mcangle_it1.291
r_angle_refined_deg1.12
r_mcbond_it0.743
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.529
r_dihedral_angle_4_deg17.248
r_dihedral_angle_3_deg12.034
r_dihedral_angle_1_deg5.427
r_scangle_it3.439
r_scbond_it2.182
r_mcangle_it1.291
r_angle_refined_deg1.12
r_mcbond_it0.743
r_nbtor_refined0.302
r_nbd_refined0.201
r_symmetry_hbond_refined0.191
r_symmetry_vdw_refined0.187
r_xyhbond_nbd_refined0.139
r_chiral_restr0.078
r_metal_ion_refined0.078
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6940
Nucleic Acid Atoms
Solvent Atoms1216
Heterogen Atoms88

Software

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