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Biosynthetic thiolase from Z. ramigera. Complex with S-pantetheine-11- pivalate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLU PDB ENTRY 1DLU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 pH 5
Crystal Properties Matthews coefficient Solvent content 3.03 59.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.32 α = 90 b = 79.15 β = 92.92 c = 150.79 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 2.65 20 95.2 0.1 11.8 3.2 57985 -3
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 2.65 2.72 98.4 0.32 3.5 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1DLU 2.65 20 52345 2756 95.28 0.23331 0.23057 0.2365 0.28571 0.285 RANDOM 64.189
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] -1.24 -0.16 -1.4 2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.6 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_4_deg 13.976 r_dihedral_angle_1_deg 5.709 r_scangle_it 2.705 r_scbond_it 1.959 r_mcangle_it 1.378 r_angle_refined_deg 1.219 r_mcbond_it 1.049 r_angle_other_deg 0.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.6 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_4_deg 13.976 r_dihedral_angle_1_deg 5.709 r_scangle_it 2.705 r_scbond_it 1.959 r_mcangle_it 1.378 r_angle_refined_deg 1.219 r_mcbond_it 1.049 r_angle_other_deg 0.889 r_symmetry_vdw_other 0.224 r_symmetry_vdw_refined 0.195 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.187 r_nbd_other 0.183 r_symmetry_hbond_refined 0.182 r_nbtor_refined 0.167 r_nbtor_other 0.085 r_chiral_restr 0.069 r_bond_refined_d 0.011 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11252 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing