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Crystal structure of LacI family transcriptional regulator from Arthrobacter sp. FB24, target EFI-560007
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 protein: 10 mM bis-tris, 500 mM NaCl, 10% glycerol, 5 mM DTT reservoir: 0.1 M magnesium chloride, 0.1 M MES:NaOH, pH 6.5, 30% (w/v) PEG 400; cryoprotection: reservoir; vapor diffusion, sitting drop, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.17 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.244 α = 90 b = 125.126 β = 96.68 c = 116.422 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 315 MIRRORS 2014-06-26 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 0.112 0.112 14.5 4.2 82386 -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 0.63 0.63 2.4 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 NONE 1.903 50 79909 2439 99.33 0.15591 0.15436 0.1688 0.20704 0.2148 RANDOM 29.492
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] 1.32 -1.13 -0.23 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.152 r_dihedral_angle_4_deg 18.685 r_scbond_it 16.313 r_scbond_other 16.312 r_scangle_other 15.617 r_long_range_B_refined 14.725 r_long_range_B_other 14.724 r_dihedral_angle_3_deg 13.63 r_mcangle_it 8.422 r_mcangle_other 8.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.152 r_dihedral_angle_4_deg 18.685 r_scbond_it 16.313 r_scbond_other 16.312 r_scangle_other 15.617 r_long_range_B_refined 14.725 r_long_range_B_other 14.724 r_dihedral_angle_3_deg 13.63 r_mcangle_it 8.422 r_mcangle_other 8.422 r_mcbond_it 8.024 r_mcbond_other 8.01 r_dihedral_angle_1_deg 5.973 r_angle_refined_deg 1.54 r_angle_other_deg 0.816 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 8008 Nucleic Acid Atoms Solvent Atoms 620 Heterogen Atoms 19
Software Software Software Name Purpose CBASS data collection SHELX model building ARP/wARP model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing