1W7V

ZnMg substituted aminopeptidase P from E. coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WL9PDB ENTRY 1WL9 WITH ALL HET ATOMS, WATERS AND MULTIPLE CONFORMERS REMOVED

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.3ROOM TEMPERATURE HANGING DROP WITH 16% PEG4K, 0.1 M TRIS (PH8.3), 0.2 M MGCL2. TRANSFERRED TO A DROP ABOVE CONDITIONS PLUS WITH 10 MM VAL-PRO-LEU PEPTIDE AND ALLOWED TO EQUILIBRATE OVERNIGHT., pH 8.30
Crystal Properties
Matthews coefficientSolvent content
4.471.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.731α = 90
b = 236.527β = 106.34
c = 137.997γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRROR2004-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
124097.90.0713.92.9225729-332.21
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)
122.0796.30.4462.7

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 1WL9 WITH ALL HET ATOMS, WATERS AND MULTIPLE CONFORMERS REMOVED237.82143281129797.90.1570.1560.18RANDOM36.28
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]
2.041.44-0.15-1.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.13
r_dihedral_angle_4_deg16.981
r_dihedral_angle_3_deg12.084
r_scangle_it8.978
r_scbond_it5.879
r_dihedral_angle_1_deg5.501
r_mcangle_it3.689
r_mcbond_it3.189
r_angle_refined_deg1.106
r_angle_other_deg0.762
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.13
r_dihedral_angle_4_deg16.981
r_dihedral_angle_3_deg12.084
r_scangle_it8.978
r_scbond_it5.879
r_dihedral_angle_1_deg5.501
r_mcangle_it3.689
r_mcbond_it3.189
r_angle_refined_deg1.106
r_angle_other_deg0.762
r_symmetry_vdw_other0.248
r_symmetry_vdw_refined0.23
r_nbd_refined0.2
r_nbd_other0.177
r_nbtor_refined0.172
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.126
r_nbtor_other0.08
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
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 Atoms14028
Nucleic Acid Atoms
Solvent Atoms1094
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing