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Crystal structure of arabinosyltransferase EmbC2-AcpM2 complex from Mycobacterium smegmatis complexed with di-arabinose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 50mM HEPES (pH 6.8~7.5), 100mM NaCl, 5-10% (v/v) polyethylene glycol 4000, 20-30% (v/v) polyethylene glycol 200
Crystal Properties Matthews coefficient Solvent content 4.24 71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.08 α = 90 b = 176.33 β = 90 c = 207.77 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 PILATUS3 S 6M 2018-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.3 134.458 99.9 0.114 0.118 0.027 12.2 19.9 67591 67591
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.48 100 5.176 5.176 5.311 1.184 0.1 19.9
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 SAD THROUGHOUT 3.3 49.67 67568 3362 100 0.234 0.232 0.2653 0.265 0.3012 RANDOM 78.18
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] 5.3329 -1.4806 -3.8522
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.3 t_omega_torsion 2.64 t_angle_deg 1.21 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 22.3 t_omega_torsion 2.64 t_angle_deg 1.21 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17088 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 228
Software Software Software Name Purpose BUSTER refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing