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Pikromycin Thioesterase adduct with reduced triketide affinity label
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MNA PDB ENTRY 1MNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 296 1.4 M Li2SO4, 100 mM HEPES 7.6, 80 mM MgCl2, 2 mM DTT, 5% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.16 61.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.898 α = 90 b = 130.728 β = 90 c = 56.484 γ = 90
Symmetry Space Group P 21 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 MARMOSAIC 300 mm CCD 2005-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97922 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 50 99 0.067 24.9 7.1 68833 68102
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.92 92.6 0.524 3.3 6.1
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 1MNA 1.85 83.33 68833 64709 3333 98.61 0.19612 0.19419 0.19 0.23219 0.2264 RANDOM 36.577
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] -1.72 -0.76 2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.909 r_dihedral_angle_3_deg 14.576 r_dihedral_angle_4_deg 13.858 r_dihedral_angle_1_deg 5.018 r_scangle_it 3.322 r_mcangle_it 3.245 r_scbond_it 2.187 r_mcbond_it 2.156 r_angle_refined_deg 1.235 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.909 r_dihedral_angle_3_deg 14.576 r_dihedral_angle_4_deg 13.858 r_dihedral_angle_1_deg 5.018 r_scangle_it 3.322 r_mcangle_it 3.245 r_scbond_it 2.187 r_mcbond_it 2.156 r_angle_refined_deg 1.235 r_nbtor_refined 0.305 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.085 r_bond_refined_d 0.01 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4245 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection SCALEPACK data scaling MOLREP phasing