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Crystal structure of a Glycerophosphoryl diester phosphodiesterase (BDI_3922) from Parabacteroides distasonis ATCC 8503 at 1.55 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 27.0000% polyethylene glycol 4000, 0.3000M ammonium sulfate, 0.1M sodium acetate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.577 α = 90 b = 90.481 β = 111.95 c = 60.373 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2009-12-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97925,0.97895 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.55 47.615 100 0.08 8.7 3.8 77355 14.681
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) 1.55 1.63 100 0.61 0.61 2.3 3.7 11285
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.55 47.615 77315 3882 99.98 0.167 0.166 0.1789 0.197 0.2078 RANDOM 19.3
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] 0.15 -0.34 -0.95 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.904 r_dihedral_angle_4_deg 14.262 r_dihedral_angle_3_deg 13.113 r_dihedral_angle_1_deg 6.129 r_scangle_it 4.029 r_scbond_it 2.535 r_angle_refined_deg 1.592 r_mcangle_it 1.402 r_angle_other_deg 0.938 r_mcbond_it 0.824
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.904 r_dihedral_angle_4_deg 14.262 r_dihedral_angle_3_deg 13.113 r_dihedral_angle_1_deg 6.129 r_scangle_it 4.029 r_scbond_it 2.535 r_angle_refined_deg 1.592 r_mcangle_it 1.402 r_angle_other_deg 0.938 r_mcbond_it 0.824 r_mcbond_other 0.283 r_chiral_restr 0.093 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4532 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHENIX phasing SOLVE phasing