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Crystal structure of the HigB1 toxin mutant K95A from Mycobacterium tuberculosis (Rv1955)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other Model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 0.1 M Na acetate pH 4.6, 30 % (w/v) PEG 4K, 0.2 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.3 46.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.975 α = 90 b = 82.054 β = 90 c = 38.047 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 4M 2020-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.9 50 98.9 0.12 0.99 9.22 6.7 11202
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 92.7 1.32 0.602 1.33
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Model 1.91 41.027 11192 560 99.299 0.215 0.2124 0.2209 0.2734 0.2778 37.644
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] -0.147 0.967 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.047 r_dihedral_angle_3_deg 17.3 r_dihedral_angle_4_deg 11.386 r_dihedral_angle_1_deg 7.301 r_lrange_it 6.408 r_lrange_other 6.322 r_scangle_it 3.855 r_scangle_other 3.841 r_mcangle_it 3.643 r_mcangle_other 3.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.047 r_dihedral_angle_3_deg 17.3 r_dihedral_angle_4_deg 11.386 r_dihedral_angle_1_deg 7.301 r_lrange_it 6.408 r_lrange_other 6.322 r_scangle_it 3.855 r_scangle_other 3.841 r_mcangle_it 3.643 r_mcangle_other 3.643 r_scbond_it 2.479 r_scbond_other 2.454 r_mcbond_other 2.42 r_mcbond_it 2.418 r_angle_refined_deg 1.833 r_angle_other_deg 1.37 r_symmetry_nbd_refined 0.231 r_nbd_other 0.224 r_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.198 r_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.182 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.087 r_symmetry_xyhbond_nbd_other 0.025 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 973 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing