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Crystal structure of LacI family transcriptional regulator from Lactobacillus casei, Target EFI-512911, with bound sucrose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.16 M calcium acetate, 0.08 M sodium cacodylate, pH 6.5, 14.4% PEG8000, 20% glycerol, cryoprotectant = reservoir + 100 mM sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.32 46.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.754 α = 90 b = 108.754 β = 90 c = 125.763 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 CCD ADSC QUANTUM 315r mirrors 2014-09-25 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 1.35 50 100 0.051 0.051 39 9.1 62512 -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 1.35 1.37 100 0.88 0.88 2.1 7.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT 1.35 44.1 60647 1865 99.94 0.11003 0.10905 0.1379 0.14093 0.1585 RANDOM 28.146
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] -0.02 -0.01 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.803 r_dihedral_angle_2_deg 34.693 r_sphericity_bonded 20.354 r_dihedral_angle_4_deg 13.154 r_dihedral_angle_3_deg 12.436 r_scbond_it 10.583 r_scbond_other 10.58 r_scangle_other 9.969 r_long_range_B_refined 8.714 r_long_range_B_other 8.713
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.803 r_dihedral_angle_2_deg 34.693 r_sphericity_bonded 20.354 r_dihedral_angle_4_deg 13.154 r_dihedral_angle_3_deg 12.436 r_scbond_it 10.583 r_scbond_other 10.58 r_scangle_other 9.969 r_long_range_B_refined 8.714 r_long_range_B_other 8.713 r_mcangle_it 6.307 r_mcangle_other 6.305 r_mcbond_it 6.19 r_mcbond_other 6.189 r_rigid_bond_restr 6 r_dihedral_angle_1_deg 5.893 r_angle_refined_deg 1.929 r_angle_other_deg 1.648 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2087 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 28
Software Software Software Name Purpose PHASER phasing ARP/wARP model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling