☰ Navigation Tabs
High resolution structure of the Lactose Repressor bound to IPTG
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 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.125 α = 90 b = 77.125 β = 90 c = 210.583 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 CCD ADSC QUANTUM 210 2006-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.92 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 83.6 0.136 10.7 43939 36802 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.06 37.5 0.264 2.1
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 2 34.04 43939 34872 1868 83.56 0.18776 0.18463 0.1879 0.24552 0.2472 RANDOM 32.852
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] 1.24 1.24 -2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.505 r_dihedral_angle_4_deg 22.436 r_dihedral_angle_3_deg 16.713 r_dihedral_angle_1_deg 7.147 r_scangle_it 4.032 r_scbond_it 2.543 r_angle_refined_deg 1.71 r_mcangle_it 1.668 r_mcbond_it 1.022 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.505 r_dihedral_angle_4_deg 22.436 r_dihedral_angle_3_deg 16.713 r_dihedral_angle_1_deg 7.147 r_scangle_it 4.032 r_scbond_it 2.543 r_angle_refined_deg 1.71 r_mcangle_it 1.668 r_mcbond_it 1.022 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.297 r_nbd_refined 0.242 r_symmetry_hbond_refined 0.225 r_xyhbond_nbd_refined 0.2 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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 4026 Nucleic Acid Atoms Solvent Atoms 738 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling PHASER phasing