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Crystal Structure of a 1.6-hexanediol Bound Tetrameric Form of Escherichia coli Lac-repressor Refined to 2.1 Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LBH PDB ENTRY 1LBH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 microseeded, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.3 46.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.15 α = 90 b = 72.434 β = 113.96 c = 130.566 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MAR scanner 300 mm plate 2001-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.93 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 119.4 100 5.9 81956
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LBH 2.1 60.06 77812 4107 99.95 0.15868 0.15639 0.20129 0.2193 RANDOM 24.938
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] -0.72 -1.46 1.39 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.353 r_dihedral_angle_4_deg 17.679 r_dihedral_angle_3_deg 15.027 r_dihedral_angle_1_deg 6.691 r_scangle_it 6.552 r_scbond_it 4.824 r_mcangle_it 2.638 r_mcbond_it 2.049 r_angle_refined_deg 1.504 r_angle_other_deg 0.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.353 r_dihedral_angle_4_deg 17.679 r_dihedral_angle_3_deg 15.027 r_dihedral_angle_1_deg 6.691 r_scangle_it 6.552 r_scbond_it 4.824 r_mcangle_it 2.638 r_mcbond_it 2.049 r_angle_refined_deg 1.504 r_angle_other_deg 0.849 r_mcbond_other 0.464 r_symmetry_vdw_other 0.336 r_symmetry_hbond_refined 0.228 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.219 r_nbd_other 0.195 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.17 r_chiral_restr 0.088 r_nbtor_other 0.086 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8964 Nucleic Acid Atoms Solvent Atoms 553 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling