3KED

Crystal structure of Aminopeptidase N in complex with 2,4-diaminobutyric acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72982.0M malonic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.5365.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.601α = 90
b = 120.601β = 90
c = 170.479γ = 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)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
12.350980.110.08779.15.76311563115
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)
12.32.3892.20.4370.59112.13.45880

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2hpo2.349.946311561036190897.580.155850.154490.19838RANDOM30.331
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]
0.630.310.63-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.754
r_dihedral_angle_4_deg21.406
r_dihedral_angle_3_deg15.168
r_dihedral_angle_1_deg6.44
r_scangle_it6.078
r_scbond_it3.857
r_mcangle_it2.054
r_angle_refined_deg1.997
r_mcbond_it1.057
r_chiral_restr0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.754
r_dihedral_angle_4_deg21.406
r_dihedral_angle_3_deg15.168
r_dihedral_angle_1_deg6.44
r_scangle_it6.078
r_scbond_it3.857
r_mcangle_it2.054
r_angle_refined_deg1.997
r_mcbond_it1.057
r_chiral_restr0.126
r_bond_refined_d0.024
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6940
Nucleic Acid Atoms
Solvent Atoms479
Heterogen Atoms86

Software

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