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Crystal Structure of the Lac Repressor bound to ONPG in repressed 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 7.5 281 1.8 M Ammonium Sulfate, 0.1 M Hepes pH 7.5. 11% PEG 400, 14% glycerol, 10X ONPG, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 5.03 75.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 253.08 α = 90 b = 253.08 β = 90 c = 203.247 γ = 120
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 mirrors 2006-03-19 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 99.89 0.176 0.176 7.3 9.1 31342 29717 -3 -3 25.4
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 3.6 99.7 0.504 0.504 4.37 6.9 2090
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 (All) 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 19.98 29717 29717 1581 99.86 0.23616 0.23616 0.23347 0.2172 0.28656 0.256 RANDOM 53.844
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 -0.01 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.867 r_dihedral_angle_3_deg 20.917 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_1_deg 5.896 r_scangle_it 1.752 r_angle_refined_deg 1.627 r_mcangle_it 0.983 r_scbond_it 0.927 r_mcbond_it 0.551 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.867 r_dihedral_angle_3_deg 20.917 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_1_deg 5.896 r_scangle_it 1.752 r_angle_refined_deg 1.627 r_mcangle_it 0.983 r_scbond_it 0.927 r_mcbond_it 0.551 r_nbtor_refined 0.308 r_nbd_refined 0.224 r_chiral_restr 0.145 r_symmetry_vdw_refined 0.144 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.108 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7418 Nucleic Acid Atoms 1046 Solvent Atoms Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing