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Crystal Structure Analysis of Aspergillus fumigatus alkaline protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 PEG 1000, PEG 3350, MPD; L-glutamate, DL-alanine, glycine, DL-lysine, and DL-serine; MOPS/HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.68 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.91 α = 90 b = 94.592 β = 103.2 c = 52.925 γ = 90
Symmetry Space Group P 1 21 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 2021-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.77115 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 38.21 95.1 0.111 0.136 0.062 0.993 5.5 4.6 22839
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 0.874 1 0.537 0.331 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 30.53 21626 1158 94.73 0.19329 0.19116 0.1913 0.22958 0.2294 RANDOM 38.513
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] -1.82 -1.7 3.43 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.392 r_dihedral_angle_4_deg 19.759 r_dihedral_angle_3_deg 17.653 r_dihedral_angle_1_deg 7.21 r_long_range_B_refined 6.97 r_scbond_it 4.083 r_mcangle_it 3.991 r_mcbond_it 2.987 r_angle_refined_deg 1.767 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.392 r_dihedral_angle_4_deg 19.759 r_dihedral_angle_3_deg 17.653 r_dihedral_angle_1_deg 7.21 r_long_range_B_refined 6.97 r_scbond_it 4.083 r_mcangle_it 3.991 r_mcbond_it 2.987 r_angle_refined_deg 1.767 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2760 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction PHASER phasing