☰ Navigation Tabs
Apo aminopeptidase P from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native aminopeptidase P without water, Mn or multiple conformers
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 298 TRIS, PEG 4000, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.4 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.322 α = 90 b = 177.322 β = 90 c = 96.312 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 1998-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200H 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 2.1 50 90.2 32.93 47221 47221 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 59.4 0.0717 2200
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 water, Mn or multiple conformers 2.1 50 45746 45746 1475 90.26 0.15036 0.14939 0.1641 0.17997 0.1905 RANDOM 18.815
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] -0.18 -0.09 -0.18 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.695 r_dihedral_angle_4_deg 14.914 r_dihedral_angle_3_deg 12.137 r_dihedral_angle_1_deg 6.09 r_scangle_it 3.884 r_mcangle_it 2.752 r_scbond_it 2.651 r_mcbond_it 2.365 r_angle_refined_deg 1.29 r_angle_other_deg 0.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.695 r_dihedral_angle_4_deg 14.914 r_dihedral_angle_3_deg 12.137 r_dihedral_angle_1_deg 6.09 r_scangle_it 3.884 r_mcangle_it 2.752 r_scbond_it 2.651 r_mcbond_it 2.365 r_angle_refined_deg 1.29 r_angle_other_deg 0.795 r_mcbond_other 0.568 r_symmetry_vdw_other 0.311 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.204 r_nbd_other 0.181 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.143 r_nbtor_other 0.081 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 456 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling