☰ Navigation Tabs
Crystal Structure of SACOL2612 - CocE/NonD family hydrolase from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3III
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 suberic acid, sebacic acid, hexadecanedioic acid, dodecanedioic acid 12mM each, PEG3350 20%, Hepes 0.1M pH 7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.221 α = 90 b = 160.583 β = 90 c = 216.827 γ = 90
Symmetry Space Group C 2 2 21
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 Mirror 2008-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9786 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.05 50 99.3 0.156 0.156 16 7.2 72687 72687 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 86.8 0.554 0.554 2.7 5.4 3155
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 (All) 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 3III 2.05 50 68929 68929 3653 99.61 0.19351 0.19351 0.1905 0.2019 0.24951 0.2599 RANDOM 8.07
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] 0.3 -3.74 3.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.134 r_dihedral_angle_4_deg 17.244 r_dihedral_angle_3_deg 14.2 r_dihedral_angle_1_deg 7.162 r_scangle_it 3.226 r_scbond_it 2.306 r_angle_other_deg 2.227 r_angle_refined_deg 1.595 r_mcangle_it 1.207 r_mcbond_it 0.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.134 r_dihedral_angle_4_deg 17.244 r_dihedral_angle_3_deg 14.2 r_dihedral_angle_1_deg 7.162 r_scangle_it 3.226 r_scbond_it 2.306 r_angle_other_deg 2.227 r_angle_refined_deg 1.595 r_mcangle_it 1.207 r_mcbond_it 0.728 r_mcbond_other 0.122 r_chiral_restr 0.1 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8937 Nucleic Acid Atoms Solvent Atoms 726 Heterogen Atoms 10
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling