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Crystal structure of Pectocin M1 from Pectobacterium carotovorum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 0.1 M HEPES pH 7.5, 19.2% w/v poly(acrylic acid sodium salt) 5,100
Crystal Properties Matthews coefficient Solvent content 2.69 54.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.279 α = 90 b = 138.553 β = 94.183 c = 68.947 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 EIGER X 16M 2023-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.04 49.49 95.5 0.077 0.993 6.63 1.82 77569 38.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.17 87.8 0.53 0.7 1.17
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4N58 2.04 49.49 1.36 77352 1976 98.58 0.1964 0.1953 0.1952 0.2385 0.2392 46.94
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 6.5369 f_angle_d 0.8471 f_chiral_restr 0.0522 f_bond_d 0.0073 f_plane_restr 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8158 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement Coot model building PHENIX phasing XDS data reduction XDS data scaling