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Crystal structure of Chromobacterium haemolyticum PE-like toxin, Hmx
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, HANGING DROP 6.5 294.15 0.12 M Monosaccharides, 0.1 M Buffer System 1 pH 6.5, 37.5 % v/v Precipitant Mix 4 (condition F4 of the Morpheus Screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.4 48.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.325 α = 90 b = 76.019 β = 90 c = 130.493 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 PIXEL DECTRIS EIGER2 XE 16M 2020-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.35 65.69 99.1 0.062 0.067 0.026 1 16.3 11.8 143804
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 1.35 1.37 90.8 1.538 1.856 1.013 0.437 0.7 5.7
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 1.35 65.686 143501 7165 98.935 0.139 0.1368 0.1367 0.173 0.1731 23.398
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] -0.217 2.139 -1.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.107 r_dihedral_angle_4_deg 16.391 r_dihedral_angle_3_deg 11.423 r_dihedral_angle_1_deg 6.689 r_lrange_it 4.559 r_lrange_other 4.215 r_rigid_bond_restr 3.744 r_scangle_it 3.605 r_scangle_other 3.605 r_scbond_it 2.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.107 r_dihedral_angle_4_deg 16.391 r_dihedral_angle_3_deg 11.423 r_dihedral_angle_1_deg 6.689 r_lrange_it 4.559 r_lrange_other 4.215 r_rigid_bond_restr 3.744 r_scangle_it 3.605 r_scangle_other 3.605 r_scbond_it 2.947 r_scbond_other 2.947 r_mcangle_it 2.878 r_mcangle_other 2.878 r_mcbond_it 2.258 r_mcbond_other 2.256 r_angle_refined_deg 1.486 r_angle_other_deg 1.435 r_nbd_refined 0.212 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.166 r_nbd_other 0.154 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_other 0.134 r_symmetry_nbd_refined 0.099 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4821 Nucleic Acid Atoms Solvent Atoms 780 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing