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4,5,6,7-tetrahydroindole in complex with T4 lysozyme L99A/M102Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LGU PDB ENTRY 1LGU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.74 55.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.327 α = 90 b = 60.327 β = 90 c = 97.438 γ = 120
Symmetry Space Group P 32 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 296 CCD ADSC QUANTUM 315r 2008-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11589 ALS 8.3.1
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 1.4 50 100 0.071 53.728 8.1 40838 40838
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) 1.4 1.45 100 0.506 4.88 8.1 4019
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 REFMAC THROUGHOUT PDB ENTRY 1LGU 1.4 50 40790 40790 2050 99.74 0.174 0.174 0.173 0.1702 0.192 0.1871 RANDOM 15.49
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] 0.16 0.08 0.16 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.507 r_dihedral_angle_3_deg 10.611 r_dihedral_angle_4_deg 9.582 r_dihedral_angle_1_deg 4.75 r_sphericity_free 2.846 r_scangle_it 2.038 r_sphericity_bonded 1.893 r_scbond_it 1.516 r_angle_refined_deg 1.14 r_mcangle_it 1.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.507 r_dihedral_angle_3_deg 10.611 r_dihedral_angle_4_deg 9.582 r_dihedral_angle_1_deg 4.75 r_sphericity_free 2.846 r_scangle_it 2.038 r_sphericity_bonded 1.893 r_scbond_it 1.516 r_angle_refined_deg 1.14 r_mcangle_it 1.011 r_rigid_bond_restr 0.887 r_mcbond_it 0.669 r_nbtor_refined 0.305 r_nbd_refined 0.191 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.149 r_symmetry_vdw_refined 0.143 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1461 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 22
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing