4KXB

Crystal structure of human aminopeptidase A complexed with bestatin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72771.6 M sodium citrate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3663.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.852α = 90
b = 141.852β = 90
c = 237.061γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2012-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.2ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.44055096

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.433.73523062789990.1750.1710.252RANDOM65.42
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]
-0.27-0.27-0.270.87
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free82.795
r_dihedral_angle_2_deg38.129
r_sphericity_bonded37.594
r_dihedral_angle_4_deg20.044
r_dihedral_angle_3_deg17.54
r_dihedral_angle_1_deg5.943
r_rigid_bond_restr1.972
r_angle_refined_deg1.261
r_chiral_restr0.084
r_bond_refined_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free82.795
r_dihedral_angle_2_deg38.129
r_sphericity_bonded37.594
r_dihedral_angle_4_deg20.044
r_dihedral_angle_3_deg17.54
r_dihedral_angle_1_deg5.943
r_rigid_bond_restr1.972
r_angle_refined_deg1.261
r_chiral_restr0.084
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7144
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms233

Software

Software
Software NamePurpose
REFMACrefinement