4FUU

Crystal structure of a leucine aminopeptidase precursor (BT_2548) from Bacteroides thetaiotaomicron VPI-5482 at 1.30 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27720.00% polyethylene glycol 3350, 0.200M ammonium dihydrogen phosphate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0840.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.236α = 65.47
b = 41.582β = 80.43
c = 48.528γ = 78.68
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315KOHZU: Double Crystal Si(111)2011-10-16MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.9537,0.9796,0.9793ALS8.2.2

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
11.327.99393.60.0557.11.9643136431312.234
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)
11.31.3391.30.4350.4351.91.94638

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 DIFFRACTIONMADTHROUGHOUT1.327.99364273326593.530.120.11810.1566RANDOM17.9771
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]
-0.17-0.140.01-0.060.6-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.544
r_dihedral_angle_4_deg21.435
r_sphericity_free12.521
r_dihedral_angle_3_deg11.458
r_scangle_it6.63
r_dihedral_angle_1_deg5.811
r_sphericity_bonded5.551
r_scbond_it4.76
r_mcangle_it3.525
r_mcbond_it2.485
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.544
r_dihedral_angle_4_deg21.435
r_sphericity_free12.521
r_dihedral_angle_3_deg11.458
r_scangle_it6.63
r_dihedral_angle_1_deg5.811
r_sphericity_bonded5.551
r_scbond_it4.76
r_mcangle_it3.525
r_mcbond_it2.485
r_rigid_bond_restr1.709
r_angle_refined_deg1.356
r_mcbond_other1.282
r_angle_other_deg0.898
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2259
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms22

Software

Software
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
SHELXDphasing