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Crystal strcuture of Acyl-CoA thioesterase from Bacillus cereus ATCC 14579
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 3.36 63.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.685 α = 90 b = 78.685 β = 90 c = 215.634 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD ADSC QUANTUM 270 2020-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.89 50 92.4 0.083 0.095 0.046 17.3 3.7 30899
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 93.1 0.367 0.415 0.189 0.94 4
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 1Y7U 2.9 30.81 29334 1531 92.34 0.1918 0.1874 0.2024 0.2764 0.2855 RANDOM 74.41
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] 2.13 1.06 2.13 -6.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.627 r_dihedral_angle_4_deg 20.796 r_dihedral_angle_3_deg 19.738 r_dihedral_angle_1_deg 7.409 r_angle_refined_deg 1.737 r_angle_other_deg 1.224 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.627 r_dihedral_angle_4_deg 20.796 r_dihedral_angle_3_deg 19.738 r_dihedral_angle_1_deg 7.409 r_angle_refined_deg 1.737 r_angle_other_deg 1.224 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7739 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 288
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction HKL-2000 data reduction