3H8G

Bestatin complex structure of leucine aminopeptidase from Pseudomonas putida


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP73000.2 M D,L Malic acid, 22.5% PEG3350 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.652.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.976α = 100.82
b = 95.989β = 107.78
c = 95.998γ = 93.23
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9340ESRFID14-1

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
11.593.65995.60.0610.0616.4451.9484972
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)
11.51.6994.60.1430.14351.9

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 REPLACEMENTTHROUGHOUT1.538.634607062426495.20.150540.149320.17345RANDOM12.953
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]
0.020.040.02-0.030.030.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.8
r_dihedral_angle_4_deg17.871
r_dihedral_angle_3_deg12.259
r_dihedral_angle_1_deg5.741
r_scangle_it4.419
r_scbond_it2.653
r_mcangle_it1.62
r_angle_refined_deg1.523
r_mcbond_it0.926
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.8
r_dihedral_angle_4_deg17.871
r_dihedral_angle_3_deg12.259
r_dihedral_angle_1_deg5.741
r_scangle_it4.419
r_scbond_it2.653
r_mcangle_it1.62
r_angle_refined_deg1.523
r_mcbond_it0.926
r_nbtor_refined0.315
r_xyhbond_nbd_refined0.238
r_nbd_refined0.237
r_symmetry_hbond_refined0.201
r_symmetry_vdw_refined0.168
r_chiral_restr0.103
r_metal_ion_refined0.094
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22084
Nucleic Acid Atoms
Solvent Atoms2974
Heterogen Atoms174

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection