3H8F

High pH native structure of leucine aminopeptidase from Pseudomonas putida


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.530015% (w/v) PEG 1500, 0.1 M PCB (Propionic acid, cacodylate, Bis-Tris Propane system) cocktail buffer, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.4950.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.786α = 68.43
b = 95.931β = 76.31
c = 96.308γ = 94.86
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.291.28796.10.3722.4166778
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3596.1

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 REPLACEMENTTHROUGHOUT2.247.451300651433493.530.197780.19190.25139RANDOM13.688
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]
0.080.11-0.03-0.020.04-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.864
r_dihedral_angle_4_deg18.244
r_dihedral_angle_3_deg16.911
r_dihedral_angle_1_deg6.261
r_scangle_it3.468
r_scbond_it2.147
r_angle_refined_deg1.53
r_mcangle_it1.32
r_mcbond_it0.726
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.864
r_dihedral_angle_4_deg18.244
r_dihedral_angle_3_deg16.911
r_dihedral_angle_1_deg6.261
r_scangle_it3.468
r_scbond_it2.147
r_angle_refined_deg1.53
r_mcangle_it1.32
r_mcbond_it0.726
r_nbtor_refined0.314
r_symmetry_vdw_refined0.268
r_nbd_refined0.239
r_xyhbond_nbd_refined0.235
r_symmetry_hbond_refined0.223
r_chiral_restr0.098
r_metal_ion_refined0.064
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 Atoms22092
Nucleic Acid Atoms
Solvent Atoms702
Heterogen Atoms42

Software

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