3N5I

Crystal structure of the precursor (S250A mutant) of the N-terminal beta-aminopeptidase BapA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N2Wsingle chain of PDB code 3N2W, w/o aa 231-250

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52771.0 - 1.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3146.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.7α = 90
b = 113.7β = 90
c = 126γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6Mdynamically bendable mirror2008-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000SLSX06SA

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
11.829.39999.10.0980.07115.644.41316883
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)
11.81.999.20.4520.4733.964.4519497

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTsingle chain of PDB code 3N2W, w/o aa 231-2501.829.3941.99131688131659263499.150.15490.15430.1801random
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]
0.94885.3411-6.2899
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.338
f_angle_d1.138
f_chiral_restr0.069
f_bond_d0.009
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10557
Nucleic Acid Atoms
Solvent Atoms1124
Heterogen Atoms49

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling