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Structure of aminopeptidase P from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AZ9 Published hexagonal structure without Mn or solvent atoms
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 277 Tris, PEG 4k, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.4 71.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.42 α = 90 b = 177.42 β = 90 c = 96.42 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 113 IMAGE PLATE RIGAKU RAXIS IIC YALE MIRRORS 1997-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.9 93 24.4 65584 -3
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 1.9 1.97 63.4 5.69
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT Published hexagonal structure without Mn or solvent atoms 1.9 38.35 63537 1991 93.06 0.15243 0.15243 0.15185 0.1641 0.17047 0.1836 RANDOM 17.996
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] 0.25 0.12 0.25 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.877 r_dihedral_angle_4_deg 15.035 r_dihedral_angle_3_deg 11.876 r_dihedral_angle_1_deg 6.042 r_scangle_it 4.006 r_mcangle_it 2.815 r_scbond_it 2.635 r_mcbond_it 2.481 r_angle_refined_deg 1.28 r_angle_other_deg 0.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.877 r_dihedral_angle_4_deg 15.035 r_dihedral_angle_3_deg 11.876 r_dihedral_angle_1_deg 6.042 r_scangle_it 4.006 r_mcangle_it 2.815 r_scbond_it 2.635 r_mcbond_it 2.481 r_angle_refined_deg 1.28 r_angle_other_deg 0.829 r_mcbond_other 0.595 r_symmetry_vdw_other 0.286 r_symmetry_hbond_refined 0.211 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.205 r_nbd_other 0.182 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.151 r_nbtor_other 0.082 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3500 Nucleic Acid Atoms Solvent Atoms 607 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling