1XRY

Crystal structure of Aeromonas proteolytica aminopeptidase in complex with bestatin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AMPPDB ENTRY 1AMP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293NaCl, KSCN, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.39α = 90
b = 107.39β = 90
c = 103.06γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293AREA DETECTORXENTRONICS1992-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODESIEMENS1.5418

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
12.129.799.10.06431.115.6208362083619.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.294.70.3392519

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1AMP2.129.692068020680204198.20.1680.1680.1640.197RANDOM23.9
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]
-0.022.86-0.020.04
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.9
c_scangle_it3.7
c_scbond_it2.63
c_mcangle_it2.45
c_mcbond_it1.64
c_angle_deg1.2
c_improper_angle_d0.8
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2210
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms24

Software

Software
Software NamePurpose
CNXrefinement
X-GENdata reduction
XDSdata scaling
X-PLORphasing