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Crystal structure of Collimonas fungivorans PE-like toxin, Cfx
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 294.15 0.2 M Magnesium chloride hexahydrate 0.1 M BIS-Tris pH 5.5, 25 % w/v PEG 3350 (condition H11 of the JCSG-plus Screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 4.31 71.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.797 α = 90 b = 141.797 β = 90 c = 202.661 γ = 120
Symmetry Space Group P 62 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 PIXEL DECTRIS EIGER2 XE 16M 2021-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.8 70.9 100 0.493 0.5 0.109 0.998 7.6 39.6 30359
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 2.8 2.95 100 5.74 5.87 1.257 0.439 0.9 41.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.8 70.9 30302 1483 99.951 0.23 0.2291 0.2304 0.2531 0.2546 83.992
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] 0.519 0.259 0.519 -1.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.252 r_dihedral_angle_6_deg 12.881 r_lrange_it 7.936 r_lrange_other 7.936 r_dihedral_angle_1_deg 6.638 r_mcangle_it 4.999 r_mcangle_other 4.999 r_dihedral_angle_2_deg 4.685 r_scangle_it 4.609 r_scangle_other 4.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.252 r_dihedral_angle_6_deg 12.881 r_lrange_it 7.936 r_lrange_other 7.936 r_dihedral_angle_1_deg 6.638 r_mcangle_it 4.999 r_mcangle_other 4.999 r_dihedral_angle_2_deg 4.685 r_scangle_it 4.609 r_scangle_other 4.608 r_mcbond_it 2.89 r_mcbond_other 2.887 r_scbond_it 2.591 r_scbond_other 2.591 r_angle_refined_deg 0.898 r_symmetry_nbd_refined 0.437 r_angle_other_deg 0.302 r_nbd_refined 0.21 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.174 r_nbd_other 0.153 r_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.041 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4699 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing