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Crystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EFA pdb entry 1EFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 281 1.4 M Sodium Acetate, 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.78 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.541 α = 90 b = 77.541 β = 90 c = 212.456 γ = 90
Symmetry Space Group P 41 21 2
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 Osmic Blue Max mirrors 2006-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 3.5 20 99.1 0.166 0.166 5.9 4.9 8745 8685 -3 -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) 3.5 3.62 99.5 0.336 0.336 3.5 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 1EFA 3.5 19.81 8745 8252 413 99.09 0.19856 0.19537 0.19 0.26516 0.2579 RANDOM 28.204
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 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.519 r_dihedral_angle_3_deg 22.382 r_dihedral_angle_4_deg 17.799 r_dihedral_angle_1_deg 8.195 r_scangle_it 3.312 r_scbond_it 1.929 r_angle_refined_deg 1.805 r_mcangle_it 1.364 r_mcbond_it 0.964 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.519 r_dihedral_angle_3_deg 22.382 r_dihedral_angle_4_deg 17.799 r_dihedral_angle_1_deg 8.195 r_scangle_it 3.312 r_scbond_it 1.929 r_angle_refined_deg 1.805 r_mcangle_it 1.364 r_mcbond_it 0.964 r_nbtor_refined 0.326 r_nbd_refined 0.27 r_symmetry_hbond_refined 0.221 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.109 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4028 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing