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Crystal structure of LacI family transcriptional regulator from Enterococcus faecium, Target EFI-512930, with bound ribose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 1 M sodium acetate:HCl, pH 4.6, 1.5 M ammonium chloride, 10 mM D-glucose, cryoprotectant = reservoir + 30% w/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.33 63.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.371 α = 90 b = 95.243 β = 119.47 c = 123.602 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315r mirrors 2014-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 50 100 0.1 0.1 16.9 5.2 197594 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 95.7 0.93 0.93 1.8 4.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.9 50 190152 5684 99.93 0.16012 0.15922 0.19234 0.2077 RANDOM 37.347
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] -1.34 0.03 2.63 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.251 r_long_range_B_other 15.084 r_long_range_B_refined 15.083 r_scangle_other 14.268 r_scbond_it 13.209 r_scbond_other 13.208 r_dihedral_angle_3_deg 12.763 r_dihedral_angle_4_deg 9.884 r_mcangle_it 8.621 r_mcangle_other 8.621
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.251 r_long_range_B_other 15.084 r_long_range_B_refined 15.083 r_scangle_other 14.268 r_scbond_it 13.209 r_scbond_other 13.208 r_dihedral_angle_3_deg 12.763 r_dihedral_angle_4_deg 9.884 r_mcangle_it 8.621 r_mcangle_other 8.621 r_mcbond_it 7.803 r_mcbond_other 7.801 r_dihedral_angle_1_deg 5.963 r_angle_refined_deg 1.22 r_angle_other_deg 0.747 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12715 Nucleic Acid Atoms Solvent Atoms 1175 Heterogen Atoms 81
Software Software Software Name Purpose SHELX model building ARP/wARP model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing