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2-nitrothiophene in complex with T4 lysozyme L99A/M102Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LGU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 277 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.74 55.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.107 α = 90 b = 60.107 β = 90 c = 96.715 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 110 CCD ADSC QUANTUM 315 Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) 2006-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.979462 SSRL BL9-1
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 1.29 52.06 99.9 0.067 11.8 7.6 51583 51583
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) 1.29 1.34 100 0.622 7.6
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 1LGU 1.29 52.06 51537 48915 2622 99.93 0.17433 0.17335 0.1711 0.19319 0.1897 RANDOM 14.447
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] -0.06 -0.03 -0.06 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.981 r_dihedral_angle_4_deg 12.315 r_dihedral_angle_3_deg 10.448 r_dihedral_angle_1_deg 4.497 r_sphericity_free 2.434 r_scangle_it 2.089 r_sphericity_bonded 1.969 r_scbond_it 1.684 r_angle_refined_deg 1.216 r_rigid_bond_restr 1.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.981 r_dihedral_angle_4_deg 12.315 r_dihedral_angle_3_deg 10.448 r_dihedral_angle_1_deg 4.497 r_sphericity_free 2.434 r_scangle_it 2.089 r_sphericity_bonded 1.969 r_scbond_it 1.684 r_angle_refined_deg 1.216 r_rigid_bond_restr 1.144 r_mcangle_it 0.989 r_mcbond_it 0.631 r_nbtor_refined 0.305 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.137 r_xyhbond_nbd_refined 0.111 r_symmetry_hbond_refined 0.075 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1331 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 21
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection REFMAC phasing