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The crystal structure of aspergilloglutamic peptidase from Aspergillus niger
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 2.7 277 1.3M AMMONIUM SULFATE, 0.1M GLYCINE BUFFER (PH 2.7), 5% (V/V) DMSO, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.692 α = 90 b = 65.842 β = 90 c = 77.391 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A Photon Factory BL-6A
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 1.6 50 95.9 0.071 12.25 37983
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 1.6 1.64 85.5 0.309 3.24
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 1Y43 1.6 38.66 37970 2010 95.9 0.21 0.208 0.2084 0.239 0.2371 RANDOM 16.38
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.568 r_dihedral_angle_3_deg 13.943 r_dihedral_angle_1_deg 7.587 r_scangle_it 3.989 r_scbond_it 2.483 r_angle_refined_deg 1.925 r_mcangle_it 1.628 r_mcbond_it 0.865 r_chiral_restr 0.093 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.568 r_dihedral_angle_3_deg 13.943 r_dihedral_angle_1_deg 7.587 r_scangle_it 3.989 r_scbond_it 2.483 r_angle_refined_deg 1.925 r_mcangle_it 1.628 r_mcbond_it 0.865 r_chiral_restr 0.093 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3017 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 8
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DENZO data reduction SCALA data scaling