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Crystal structure of PknD-34, a repeat fragment from the M. tuberculosis PknD beta-propeller
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.36 63.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.351 α = 90 b = 95.351 β = 90 c = 69.829 γ = 120
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 16M 2018-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.0000 SOLEIL PROXIMA 1
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 1.7 47.68 90.5 0.098 0.102 0.025 0.999 19.5 17 36012 20.31
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 1.7 1.73 100 0.858 0.882 0.203 0.925 18.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 32.16 1.34 35964 1711 90.42 0.1942 0.1933 0.1934 0.2131 0.2135 28.01
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 12.2954 f_angle_d 1.1855 f_chiral_restr 0.0858 f_plane_restr 0.0128 f_bond_d 0.0096
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1784 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing