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Crystal structure of Zinc-binding metallopeptidase (Uniprot: A0AAN3A8D2) from Bacteroides ovatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold A0AAN3A8D2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 0.2M Magnesium formate, dihydrate, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.83 32.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.314 α = 90 b = 66.81 β = 90 c = 99.072 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 100 CCD MARMOSAIC 225 mm CCD Mirrors 2022-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97777 RRCAT INDUS-2 PX-BL21
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 49.54 100 0.116 0.125 0.047 0.998 13.1 7.1 19700 23.96
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 2.05 100 0.766 0.825 0.305 0.904 2.7 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 38.91 1.34 16937 799 99.47 0.2268 0.2248 0.2247 0.2679 0.2678 33.56
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 f_dihedral_angle_d 17.6452 f_angle_d 0.5483 f_chiral_restr 0.0428 f_plane_restr 0.0056 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1961 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX model building PHENIX refinement Coot model building