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Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch Crystallization 7.5 295 30%(v/v) 2-Propanol, 0.1M Hepes 7.5, 0.2M MgCl2, 10mM Spermidine, 0.1mM ZnCl2, microbatch Crystallization, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.52 51.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.02 α = 90 b = 218.267 β = 90 c = 172.693 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS V 2009-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45PX 1.7321 SPring-8 BL45PX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.44 50 99.1 95594 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.64 99.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4NJR 2.44 48.79 95594 5026 95.97 0.15044 0.14799 0.1662 0.1965 0.2057 RANDOM 39.364
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] -3.71 2.53 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.534 r_dihedral_angle_4_deg 18.817 r_dihedral_angle_3_deg 15.86 r_dihedral_angle_1_deg 7.387 r_angle_refined_deg 1.743 r_angle_other_deg 0.852 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.534 r_dihedral_angle_4_deg 18.817 r_dihedral_angle_3_deg 15.86 r_dihedral_angle_1_deg 7.387 r_angle_refined_deg 1.743 r_angle_other_deg 0.852 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 Atoms Number Protein Atoms 18936 Nucleic Acid Atoms Solvent Atoms 890 Heterogen Atoms 6
Software Software Software Name Purpose HKL-2000 data collection CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing