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AM0627 metallopeptidase from Akkermansia muciniphila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KD5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 PEG 4000, glycerol, HEPES/MOPS, alcohols
Crystal Properties Matthews coefficient Solvent content 3.09 60.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.564 α = 90 b = 101.564 β = 90 c = 114.626 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 PIXEL DECTRIS PILATUS 6M Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 2020-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.9 87.957 99.9 0.105 0.118 0.052 8.9 4.9 52780 52780
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 99.8 0.738 0.738 0.855 0.425 1.1 3.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5KD5 1.9 29.96 50020 2666 99.83 0.1713 0.1697 0.2023 0.1953 RANDOM 31.165
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] 0.76 0.38 0.76 -2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.105 r_dihedral_angle_4_deg 16.425 r_dihedral_angle_3_deg 16.377 r_dihedral_angle_1_deg 5.802 r_angle_refined_deg 1.552 r_chiral_restr 0.108 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3895 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 36
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction