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Crystal structure of lipoate protein ligase from Mycoplasma hyopneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 289 0.2 M (NH4)2SO4, 0.1 M sodium acetate pH 4.0, 20% PEG 2000 MME
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.322 α = 90 b = 100.322 β = 90 c = 155.587 γ = 90
Symmetry Space Group P 41 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 16M 2018-11-12 M SINGLE WAVELENGTH 2 2 x-ray 100 PIXEL DECTRIS PILATUS 6M 2018-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97894 SSRF BL17U1 2 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97891 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.45 50 99.6 0.06 0.062 0.016 13.4 14.9 31325
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 2.45 2.54 99.1 0.758 0.785 0.193 0.903 14.9
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 (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 2.45 43.15 28111 1473 98.83 0.204 0.2007 0.2022 0.2683 0.2689 RANDOM 67.06
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] -0.79 -0.79 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.598 r_dihedral_angle_3_deg 20.444 r_dihedral_angle_4_deg 17.118 r_dihedral_angle_1_deg 6.843 r_angle_refined_deg 1.753 r_chiral_restr 0.119 r_gen_planes_refined 0.01 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5425 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing SHELX phasing DM phasing PDB_EXTRACT data extraction