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Pikromycin thioesterase in complex with product 10-deoxymethynolide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MNA PDB id: 1MNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 296 1.4M Li2SO4, 80mM MgCl2, 100mM HEPES pH 7.6, 2mM DTT, 5% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.01 59.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.051 α = 90 b = 131.076 β = 90 c = 57.512 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 2005-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 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 1.79 50 94.4 0.069 23.16 6.6 73552
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) 1.79 1.85 68.1 0.47 2.3 3.8
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 id: 1MNA 1.79 50 77946 69888 3566 94.21 0.19406 0.19216 0.1894 0.22972 0.2261 RANDOM 31.695
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] -0.96 -0.49 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.528 r_dihedral_angle_4_deg 15.357 r_dihedral_angle_3_deg 13.687 r_dihedral_angle_1_deg 4.964 r_scangle_it 2.998 r_mcangle_it 2.877 r_scbond_it 1.951 r_mcbond_it 1.878 r_angle_refined_deg 1.172 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.528 r_dihedral_angle_4_deg 15.357 r_dihedral_angle_3_deg 13.687 r_dihedral_angle_1_deg 4.964 r_scangle_it 2.998 r_mcangle_it 2.877 r_scbond_it 1.951 r_mcbond_it 1.878 r_angle_refined_deg 1.172 r_nbtor_refined 0.303 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.077 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 4267 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 74
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing