2V3X

His243Ala Escherichia coli aminopeptidase P in complex with substrate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5277CRYSTALLISED IN 30% PEG 4K, 0.1 M TRIS PH 8.5 AT 277K. SOAKED IN 30% PEG 4K, 0.1 M TRIS PH 8.5, 1 MM MNCL2, 5 MM VAL-PRO-LEU, 10% MPD FOR 30 MIN AT 277K IMMEDIATELY PRIOR TO DATA COLLECTION.
Crystal Properties
Matthews coefficientSolvent content
4.472

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.396α = 90
b = 177.396β = 90
c = 96.499γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2006-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-ID-B

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
11.75097.70.0620.94.695461-321.96
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7698.30.344.44.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1WL91.730.0692522289297.70.1410.1410.154RANDOM13.51
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]
-0.03-0.02-0.030.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.196
r_dihedral_angle_4_deg15.338
r_dihedral_angle_3_deg10.727
r_dihedral_angle_1_deg5.824
r_scangle_it5.323
r_scbond_it3.618
r_mcangle_it2.073
r_mcbond_it1.883
r_angle_refined_deg1.288
r_angle_other_deg0.911
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.196
r_dihedral_angle_4_deg15.338
r_dihedral_angle_3_deg10.727
r_dihedral_angle_1_deg5.824
r_scangle_it5.323
r_scbond_it3.618
r_mcangle_it2.073
r_mcbond_it1.883
r_angle_refined_deg1.288
r_angle_other_deg0.911
r_symmetry_vdw_other0.315
r_symmetry_vdw_refined0.303
r_nbd_refined0.208
r_nbd_other0.195
r_nbtor_refined0.175
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.143
r_chiral_restr0.082
r_nbtor_other0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3518
Nucleic Acid Atoms
Solvent Atoms644
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing