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Glu383Ala Escherichia coli aminopeptidase P in complex with substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WL9 PDB ENTRY 1WL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 CRYSTALLISED IN 30% PEG 4K, 0.1 M TRIS PH 8.8 AT 277K. SOAKED IN 30% PEG 4K, 0.1 M TRIS PH 8.5, 1 MM MNCL2, 5 MM VAL-PRO-LEU, 10% MPD FOR 30 MIN AT 277K IMMEDIATELY PRIOR TO DATA COLLECTION.
Crystal Properties Matthews coefficient Solvent content 4.4 72.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.695 α = 90 b = 177.695 β = 90 c = 96.433 γ = 120
Symmetry Space Group P 64 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD MIRRORS 2006-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.56 50 99.4 0.07 32.5 11 125677 -3 17.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.62 99.8 0.58 4.3 10
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WL9 1.56 29.66 121838 3825 99.4 0.14 0.14 0.15 RANDOM 10.84
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] 0.11 0.05 0.11 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.315 r_dihedral_angle_4_deg 16.367 r_dihedral_angle_3_deg 11.156 r_dihedral_angle_1_deg 5.832 r_scangle_it 5.7 r_scbond_it 3.923 r_mcangle_it 2.396 r_mcbond_it 2.206 r_angle_refined_deg 1.348 r_angle_other_deg 0.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.315 r_dihedral_angle_4_deg 16.367 r_dihedral_angle_3_deg 11.156 r_dihedral_angle_1_deg 5.832 r_scangle_it 5.7 r_scbond_it 3.923 r_mcangle_it 2.396 r_mcbond_it 2.206 r_angle_refined_deg 1.348 r_angle_other_deg 0.902 r_symmetry_vdw_refined 0.358 r_symmetry_vdw_other 0.326 r_nbd_refined 0.217 r_nbd_other 0.195 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.126 r_nbtor_other 0.084 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3519 Nucleic Acid Atoms Solvent Atoms 731 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing