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Crystal structure of yeast aminopeptidase 1 (Ape1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 0.1M Tris-HCl pH7.2, 1.1M NaCl, 42.5% PEG 400, 0.1M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 3.18 61.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.171 α = 90 b = 140.171 β = 90 c = 348.677 γ = 120
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 RAYONIX MX300HE 2014-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A 1.2 NSRRC BL15A
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 2.5 116.23 96.56 87912 84889 2
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 2.5 2.59 98 0.554 2.04
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 4DYO 2.5 116.23 80667 4222 95.69 0.2169 0.21532 0.2174 0.24637 0.2452 RANDOM 42.309
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] 0.09 0.05 0.09 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.785 r_dihedral_angle_4_deg 19.996 r_dihedral_angle_3_deg 19.056 r_dihedral_angle_1_deg 6.245 r_long_range_B_refined 4.199 r_long_range_B_other 4.199 r_mcangle_it 2.359 r_mcangle_other 2.359 r_scangle_other 1.886 r_mcbond_it 1.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.785 r_dihedral_angle_4_deg 19.996 r_dihedral_angle_3_deg 19.056 r_dihedral_angle_1_deg 6.245 r_long_range_B_refined 4.199 r_long_range_B_other 4.199 r_mcangle_it 2.359 r_mcangle_other 2.359 r_scangle_other 1.886 r_mcbond_it 1.295 r_mcbond_other 1.295 r_angle_refined_deg 1.092 r_scbond_it 1.018 r_scbond_other 1.018 r_angle_other_deg 0.726 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13544 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling