2BHB

Zn substituted E. coli Aminopeptidase P


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
1VAPOR DIFFUSION, HANGING DROP7277AMINOPEPTIDASE 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 BY HANGING DROP VAPOUR DIFFUSION. CRYSTALS WERE SOAKED FOR 2 HOURS IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM ZNCL2 PRIOR TO DATA COLLECTION.
Crystal Properties
Matthews coefficientSolvent content
5.677.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.814α = 90
b = 138.814β = 90
c = 230.914γ = 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
12.46098.90.0722.26.243879-355.61
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)
12.42.49910.493.44.7

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 1N51 STRIPPED OF MULTIPLE CONFORMERS, SOLVENT ATOMS AND HETERO COMPOUNDS2.4160.1941450212699.40.1680.1670.19RANDOM46.55
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]
1.451.45-2.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.237
r_dihedral_angle_4_deg15.701
r_dihedral_angle_3_deg12.062
r_dihedral_angle_1_deg5.942
r_scangle_it4.663
r_scbond_it2.95
r_mcangle_it1.611
r_mcbond_it1.162
r_angle_refined_deg1.113
r_angle_other_deg0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.237
r_dihedral_angle_4_deg15.701
r_dihedral_angle_3_deg12.062
r_dihedral_angle_1_deg5.942
r_scangle_it4.663
r_scbond_it2.95
r_mcangle_it1.611
r_mcbond_it1.162
r_angle_refined_deg1.113
r_angle_other_deg0.75
r_symmetry_vdw_other0.251
r_symmetry_vdw_refined0.244
r_nbd_refined0.189
r_nbd_other0.169
r_nbtor_refined0.169
r_symmetry_hbond_refined0.143
r_xyhbond_nbd_refined0.128
r_metal_ion_refined0.085
r_nbtor_other0.079
r_chiral_restr0.061
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_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 Atoms216
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling