2BN7

Mn substituted E. coli Aminopeptidase P in complex with product and Zn


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
17.5277AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN IN 22% MPD, 100 MM NACITRATE (PH 7.5) AND 200 MM MGACETATE AT 4C. CRYSTALS WERE SOAKED FOR 1 HOUR IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM MNCL2, 1 MM ZNCL2 AND 10 MM PROLEU DIPEPTIDE PRIOR TO DATA COLLECTION.
Crystal Properties
Matthews coefficientSolvent content
5.2576.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.695α = 90
b = 139.695β = 90
c = 230.674γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRRORS2005-03-18MSINGLE 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
12.4601000.0725.48.744853-355.06
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)
12.42.4999.70.543.27

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 COMPOUNDS2.4119.5242588218499.80.1660.1650.187RANDOM48
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]
1.411.41-2.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.909
r_dihedral_angle_4_deg16.028
r_dihedral_angle_3_deg11.47
r_dihedral_angle_1_deg5.985
r_scangle_it3.101
r_scbond_it2.005
r_mcangle_it1.211
r_angle_refined_deg1.087
r_mcbond_it0.829
r_angle_other_deg0.754
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.909
r_dihedral_angle_4_deg16.028
r_dihedral_angle_3_deg11.47
r_dihedral_angle_1_deg5.985
r_scangle_it3.101
r_scbond_it2.005
r_mcangle_it1.211
r_angle_refined_deg1.087
r_mcbond_it0.829
r_angle_other_deg0.754
r_symmetry_vdw_refined0.26
r_symmetry_vdw_other0.219
r_nbd_refined0.188
r_nbd_other0.169
r_nbtor_refined0.167
r_symmetry_hbond_refined0.138
r_xyhbond_nbd_refined0.123
r_nbtor_other0.08
r_chiral_restr0.059
r_bond_refined_d0.008
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 Atoms286
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling