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Glu383Ala Escherichia coli Aminopeptidase P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BHC PDB ENTRY 2BHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 SITTING DROP VAPOUR DIFFUSION AT 4C. 2 UL 17 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 30% MPD, 0.1 M CITRATE PH 7.5, 0.2 M MGACETATE. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM MNCL2 FOR 45 MIN AT 4C PRIOR TO CRYOCOOLING.
Crystal Properties Matthews coefficient Solvent content 5.6 77.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.578 α = 90 b = 138.578 β = 90 c = 231.389 γ = 90
Symmetry Space Group I 41 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 IMAGE PLATE MARRESEARCH OSMIC MIRRORS 2005-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200H
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 2.4 60 94.1 0.11 13.9 5.9 41368 6 40.42
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 2.4 2.53 91.3 0.55 2.5 4.5
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 PDB ENTRY 2BHC 2.4 119.52 39342 2026 93.5 0.174 0.172 0.1815 0.207 0.214 RANDOM 38.44
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] 1.09 1.09 -2.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.002 r_dihedral_angle_4_deg 15.65 r_dihedral_angle_3_deg 12.88 r_dihedral_angle_1_deg 5.909 r_scangle_it 2.985 r_scbond_it 1.887 r_mcangle_it 1.219 r_angle_refined_deg 1.178 r_mcbond_it 0.819 r_angle_other_deg 0.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.002 r_dihedral_angle_4_deg 15.65 r_dihedral_angle_3_deg 12.88 r_dihedral_angle_1_deg 5.909 r_scangle_it 2.985 r_scbond_it 1.887 r_mcangle_it 1.219 r_angle_refined_deg 1.178 r_mcbond_it 0.819 r_angle_other_deg 0.755 r_symmetry_vdw_other 0.255 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.195 r_nbtor_refined 0.172 r_nbd_other 0.17 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.13 r_nbtor_other 0.08 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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 3483 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling