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Crystal strcture of PirA insecticidal protein from Photorhabdus akhurstii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3X0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 0.8 M Potasium sodium tartrate tetrahydrate, 0.1 M Tris-Cl pH 8.5, 0.5 % (w/v) Polyethelene glycol MME
Crystal Properties Matthews coefficient Solvent content 1.82 32.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.775 α = 90 b = 118.775 β = 90 c = 53.873 γ = 90
Symmetry Space Group P 41 2 2
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 Mirror 2021-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.9789 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 1.6 37.56 100 0.074 0.076 0.015 1 34.6 26.1 51378 19.21
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 1.6 1.63 100 1.353 1.379 0.268 0.857 3 26.2
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 3X0T 1.6 37.56 1.34 51337 2555 99.97 0.1673 0.1659 0.1655 0.1939 0.1949 23.81
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 8.7658 f_angle_d 0.8566 f_chiral_restr 0.0633 f_plane_restr 0.0076 f_bond_d 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3166 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 115
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX model building PHENIX refinement Coot model building