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Crystal structure of phospholipase/Carboxylesterase from Dyadobacter fermentans DSM 18053
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 297 0.1 M tri sodium citrate, 20% PEG4000, 5% iso-propanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.18 43.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.157 α = 72.77 b = 40.251 β = 78.37 c = 67.256 γ = 76.09
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 2012-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
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 1.62 63.6 96.8 0.089 22 96.8 49246 47679 -3
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 1.62 1.63 94 0.43 2.15 3 1166
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.62 63.6 47507 47507 2412 96.05 0.1391 0.1391 0.1362 0.1437 0.194 0.1947 RANDOM 20.7163
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] 0.04 0.2 -1.17 -0.68 -0.49 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.469 r_sphericity_free 29.274 r_dihedral_angle_4_deg 18.612 r_sphericity_bonded 13.473 r_dihedral_angle_3_deg 12.22 r_dihedral_angle_1_deg 5.886 r_rigid_bond_restr 2.361 r_angle_refined_deg 1.293 r_chiral_restr 0.092 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.469 r_sphericity_free 29.274 r_dihedral_angle_4_deg 18.612 r_sphericity_bonded 13.473 r_dihedral_angle_3_deg 12.22 r_dihedral_angle_1_deg 5.886 r_rigid_bond_restr 2.361 r_angle_refined_deg 1.293 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3174 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MLPHARE phasing DM phasing SHELXDE phasing ARP/wARP model building RESOLVE phasing Coot model building