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Mg-substituted form of E. coli aminopeptidase P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NATIVE AMINOPEPTIDASE P WITHOUT HETATOMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP TRIS, PEG 4000, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 4.4 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.733 α = 90 b = 177.733 β = 90 c = 96.484 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 1998-08-24 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 2 42.26 92.4 26.53 56174 56174 -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 2 2.05 64.2 5.39
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT NATIVE AMINOPEPTIDASE P WITHOUT HETATOMS 2 42.26 54464 54464 1708 92.44 0.14832 0.14751 0.1615 0.17336 0.1836 RANDOM 17.504
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] -0.13 -0.06 -0.13 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.765 r_dihedral_angle_4_deg 15.015 r_dihedral_angle_3_deg 12.207 r_dihedral_angle_1_deg 6.003 r_scangle_it 3.878 r_mcangle_it 2.695 r_scbond_it 2.53 r_mcbond_it 2.371 r_angle_refined_deg 1.296 r_angle_other_deg 0.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.765 r_dihedral_angle_4_deg 15.015 r_dihedral_angle_3_deg 12.207 r_dihedral_angle_1_deg 6.003 r_scangle_it 3.878 r_mcangle_it 2.695 r_scbond_it 2.53 r_mcbond_it 2.371 r_angle_refined_deg 1.296 r_angle_other_deg 0.797 r_mcbond_other 0.57 r_symmetry_vdw_other 0.283 r_symmetry_vdw_refined 0.282 r_nbd_refined 0.207 r_nbd_other 0.181 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.145 r_nbtor_other 0.081 r_chiral_restr 0.074 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 3499 Nucleic Acid Atoms Solvent Atoms 599 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling