2BH3

Zn substituted E. coli Aminopeptidase P in complex with product


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N51PDB ENTRY 1N51 STRIPPED OF MULTIPLE CONFORMERS, SOLVENT ATOMS AND HETERO COMPOUNDS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17277AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN IN 26% MPD, 100 MM NACITRATE (PH 7.0) AND 200 MM MGACETATE AT 4C. CRYSTALS WERE SOAKED FOR 2 HOURS IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM ZNCL2 AND 10 MM PROLEU DIPEPTIDE PRIOR TO DATA COLLECTION.
Crystal Properties
Matthews coefficientSolvent content
5.3276.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.012α = 90
b = 138.012β = 90
c = 230.734γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRRORS2004-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200H

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
12.46099.20.0525.26.143466-355.02
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)
12.42.4998.50.523.25

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 1N51 STRIPPED OF MULTIPLE CONFORMERS, SOLVENT ATOMS AND HETERO COMPOUNDS2.460.1941151209998.80.1750.1740.201RANDOM47.17
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]
1.581.58-3.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.372
r_dihedral_angle_4_deg16.164
r_dihedral_angle_3_deg12.067
r_dihedral_angle_1_deg6.055
r_scangle_it3.879
r_scbond_it2.522
r_mcangle_it1.542
r_mcbond_it1.131
r_angle_refined_deg1.117
r_angle_other_deg0.755
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.372
r_dihedral_angle_4_deg16.164
r_dihedral_angle_3_deg12.067
r_dihedral_angle_1_deg6.055
r_scangle_it3.879
r_scbond_it2.522
r_mcangle_it1.542
r_mcbond_it1.131
r_angle_refined_deg1.117
r_angle_other_deg0.755
r_symmetry_vdw_other0.269
r_symmetry_vdw_refined0.245
r_nbd_refined0.193
r_nbd_other0.17
r_nbtor_refined0.169
r_symmetry_hbond_refined0.133
r_xyhbond_nbd_refined0.117
r_nbtor_other0.081
r_chiral_restr0.063
r_bond_refined_d0.009
r_gen_planes_refined0.003
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 Atoms3487
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling