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Crystal structure of phosphorylated Ser78 form of Rv1045 toxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C46
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 2.4M ammonium phosphate dibasic, 0.1M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.48 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.42 α = 90 b = 94.42 β = 90 c = 61.91 γ = 120
Symmetry Space Group P 32 2 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 PILATUS 6M 2020-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.97790 ELETTRA 11.2C
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 81.77 100 0.087 0.092 0.029 1 24.3 19.1 42300 18.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 1.389 1.43 0.786 17.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7C46 1.6 81.77 40210 2088 99.98 0.18727 0.18519 0.1889 0.22718 0.2289 RANDOM 29.181
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] 1.78 0.89 1.78 -5.76
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.858 r_dihedral_angle_2_deg 30.218 r_sphericity_bonded 26.915 r_dihedral_angle_4_deg 14.893 r_dihedral_angle_3_deg 12.916 r_long_range_B_refined 5.808 r_dihedral_angle_1_deg 5.259 r_long_range_B_other 5.201 r_mcangle_other 3.85 r_mcangle_it 3.848
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.858 r_dihedral_angle_2_deg 30.218 r_sphericity_bonded 26.915 r_dihedral_angle_4_deg 14.893 r_dihedral_angle_3_deg 12.916 r_long_range_B_refined 5.808 r_dihedral_angle_1_deg 5.259 r_long_range_B_other 5.201 r_mcangle_other 3.85 r_mcangle_it 3.848 r_scangle_other 3.699 r_scbond_it 3.132 r_scbond_other 3.039 r_mcbond_it 2.965 r_mcbond_other 2.955 r_rigid_bond_restr 1.801 r_angle_refined_deg 1.233 r_angle_other_deg 0.747 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2222 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing