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Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native C. elegans APP-1 structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 0.2 M sodium iodide, 0.1 M Bis-Tris propane, pH 7.5, 20 % w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.15 42.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.59 α = 90 b = 86.81 β = 115.96 c = 113.13 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.968 Diamond I24
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 2.15 38.52 91.8 0.063 13.3 2.6 61133 61133 2 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 2.15 2.21 60.4 0.453 2.4 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT native C. elegans APP-1 structure 2.15 38.52 61133 58022 3099 91.7 0.20668 0.20451 0.2474 0.236 RANDOM 35.227
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.847 r_dihedral_angle_3_deg 15.187 r_dihedral_angle_4_deg 14.165 r_dihedral_angle_1_deg 5.633 r_long_range_B_refined 5.003 r_long_range_B_other 5.003 r_scangle_other 3.325 r_mcangle_other 2.848 r_mcangle_it 2.792 r_scbond_it 2.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.847 r_dihedral_angle_3_deg 15.187 r_dihedral_angle_4_deg 14.165 r_dihedral_angle_1_deg 5.633 r_long_range_B_refined 5.003 r_long_range_B_other 5.003 r_scangle_other 3.325 r_mcangle_other 2.848 r_mcangle_it 2.792 r_scbond_it 2.167 r_scbond_other 2.139 r_mcbond_it 1.768 r_mcbond_other 1.768 r_angle_refined_deg 1.227 r_angle_other_deg 0.876 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 9799 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 39
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling