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Crystal structure of LacI family transcriptional regulator from Arthrobacter sp. FB24, target EFI-560007, complex with lactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RKQ
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:HAOH, pH 6.5, 30% (w/v) PEG 400; cryoprotection: reservoir plus 20 mM lactose; vapor diffusion, sitting drop, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.16 43.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.936 α = 90 b = 124.912 β = 96.51 c = 117.043 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 2014-07-10 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 2.2 50 99.1 0.141 0.141 7.5 3 52910 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.23 98.6 1.4 3
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 MOLECULAR REPLACEMENT THROUGHOUT 4RKQ 2.2 50 51293 1588 98.9 0.17387 0.17142 0.179 0.25183 0.2506 RANDOM 45.889
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] 1.8 -2.3 0.29 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.043 r_scbond_it 20.971 r_scbond_other 20.971 r_scangle_other 20.179 r_long_range_B_refined 18.724 r_long_range_B_other 18.724 r_dihedral_angle_4_deg 17.766 r_dihedral_angle_3_deg 13.34 r_mcbond_other 12.589 r_mcbond_it 12.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.043 r_scbond_it 20.971 r_scbond_other 20.971 r_scangle_other 20.179 r_long_range_B_refined 18.724 r_long_range_B_other 18.724 r_dihedral_angle_4_deg 17.766 r_dihedral_angle_3_deg 13.34 r_mcbond_other 12.589 r_mcbond_it 12.579 r_mcangle_other 12.343 r_mcangle_it 12.341 r_dihedral_angle_1_deg 5.852 r_angle_refined_deg 1.2 r_angle_other_deg 0.71 r_chiral_restr 0.062 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 7956 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 92
Software Software Software Name Purpose CBASS data collection PHASER phasing ARP/wARP model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling