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Crystal structure of acyl-CoA thioesterase tesB from Yersinia pestis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C8U pdb entry 1C8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 296 20% PEG3350, 235mM sodium malonate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.33 47.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.23 α = 90 b = 171.62 β = 109.62 c = 73.7 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 ADSC QUANTUM 315r 2012-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 54.29 93.68 0.103 10.3 5.9 446767 75550
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 2.04 87.3 0.211 5.6 6.1 4191
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 1C8U 2 24.29 71671 71671 3827 93.68 0.22313 0.22071 0.2269 0.26813 0.2703 RANDOM 29.875
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] -0.01 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.366 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 15.132 r_dihedral_angle_1_deg 6.907 r_long_range_B_other 6.188 r_long_range_B_refined 6.184 r_scangle_other 4.373 r_mcangle_it 3.807 r_mcangle_other 3.807 r_scbond_it 2.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.366 r_dihedral_angle_4_deg 17.36 r_dihedral_angle_3_deg 15.132 r_dihedral_angle_1_deg 6.907 r_long_range_B_other 6.188 r_long_range_B_refined 6.184 r_scangle_other 4.373 r_mcangle_it 3.807 r_mcangle_other 3.807 r_scbond_it 2.892 r_scbond_other 2.892 r_mcbond_it 2.604 r_mcbond_other 2.604 r_angle_refined_deg 1.685 r_angle_other_deg 0.875 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8460 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction Aimless data scaling