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Crystal structure of Cj0915, a hexameric hotdog fold thioesterase of Campylobacter jejuni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YLI pdb entry 1YLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 288 0.75M NaCl, 0.1M Sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.08 60.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.018 α = 90 b = 103.018 β = 90 c = 103.018 γ = 90
Symmetry Space Group P 41 3 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 2007-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97915 APS 19-BM
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 2.59 50 100 0.104 5.6 19.1 6240
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) 2.59 2.69 100 0.339 13.9
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 1YLI 2.59 24.28 5920 286 100 0.20893 0.20651 0.2032 0.25971 0.2543 RANDOM 23.323
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.055 r_dihedral_angle_3_deg 19.591 r_dihedral_angle_4_deg 15.418 r_dihedral_angle_1_deg 6.253 r_scangle_it 2.134 r_angle_refined_deg 1.263 r_scbond_it 1.169 r_mcangle_it 1.058 r_mcbond_it 0.575 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.055 r_dihedral_angle_3_deg 19.591 r_dihedral_angle_4_deg 15.418 r_dihedral_angle_1_deg 6.253 r_scangle_it 2.134 r_angle_refined_deg 1.263 r_scbond_it 1.169 r_mcangle_it 1.058 r_mcbond_it 0.575 r_nbtor_refined 0.298 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.116 r_xyhbond_nbd_refined 0.103 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 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 1002 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction SCALEPACK data scaling MOLREP phasing