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Crystal structure of oxidized form of thiolase from Clostridium acetobutylicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 295 PEG 3350, K-citrate, NaCl
Crystal Properties Matthews coefficient Solvent content 2.42 49.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 203.227 α = 90 b = 53.987 β = 90 c = 72.968 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 ADSC QUANTUM 210 2008-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.23985 PAL/PLS 7A (6B, 6C1)
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 1.77 50 98.1 0.07 33.7 5.3 79061
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 1.77 1.83 87.9 0.299 2.8 4.1
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 1DLV 1.77 50 73992 3911 98.54 0.15662 0.15479 0.1696 0.19102 0.1986 RANDOM 32.174
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] -1.69 3.2 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.594 r_dihedral_angle_3_deg 15.176 r_dihedral_angle_4_deg 13.394 r_long_range_B_refined 7.697 r_long_range_B_other 7.577 r_dihedral_angle_1_deg 6.538 r_scangle_other 5.91 r_scbond_it 3.931 r_scbond_other 3.919 r_mcangle_it 3.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.594 r_dihedral_angle_3_deg 15.176 r_dihedral_angle_4_deg 13.394 r_long_range_B_refined 7.697 r_long_range_B_other 7.577 r_dihedral_angle_1_deg 6.538 r_scangle_other 5.91 r_scbond_it 3.931 r_scbond_other 3.919 r_mcangle_it 3.816 r_mcangle_other 3.815 r_mcbond_it 2.719 r_mcbond_other 2.714 r_angle_refined_deg 1.811 r_angle_other_deg 0.893 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5674 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing