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Jack bean asparaginyl endopeptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 HEPES, PEG 20,000, EDTA disodium salt dihydrate
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.989 α = 90 b = 88.882 β = 111.722 c = 109.848 γ = 90
Symmetry Space Group I 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 EIGER X 16M 2018-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.984 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.69 46.33 98.8 0.997 9.6 3.4 26353
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.82 0.662
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5NIJ 2.69 45.611 26351 1323 98.737 0.2 0.1958 0.2683 0.259 69.426
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] -5.007 -1.323 1.247 3.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.15 r_dihedral_angle_3_deg 18.136 r_dihedral_angle_4_deg 11.748 r_lrange_it 8.187 r_lrange_other 8.186 r_dihedral_angle_1_deg 6.955 r_mcangle_it 5.847 r_mcangle_other 5.846 r_scangle_it 5.466 r_scangle_other 5.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.15 r_dihedral_angle_3_deg 18.136 r_dihedral_angle_4_deg 11.748 r_lrange_it 8.187 r_lrange_other 8.186 r_dihedral_angle_1_deg 6.955 r_mcangle_it 5.847 r_mcangle_other 5.846 r_scangle_it 5.466 r_scangle_other 5.465 r_mcbond_it 3.751 r_mcbond_other 3.751 r_scbond_it 3.443 r_scbond_other 3.443 r_angle_refined_deg 1.355 r_angle_other_deg 1.126 r_nbd_other 0.257 r_nbd_refined 0.203 r_symmetry_nbd_other 0.176 r_symmetry_nbd_refined 0.172 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.081 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.051 r_symmetry_xyhbond_nbd_other 0.007 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6750 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Coot model building Aimless data scaling