☰ Navigation Tabs
Crystal structure of a glycerophosphodiester phosphodiesterase (BDI_0402) from Parabacteroides distasonis ATCC 8503 at 1.89 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2000M magnesium chloride, 30.0000% polyethylene glycol 4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 48.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.46 α = 90 b = 40.876 β = 99.39 c = 48.328 γ = 90
Symmetry Space Group C 1 2 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 collimating mirror, toroid focusing mirror 2010-05-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97941,0.97915 SSRL BL9-2
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 1.89 26.955 97.5 0.055 8.97 21375 -3 22.126
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) 1.89 1.96 96.1 0.307 2.3
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 1.89 26.955 21374 1099 99.42 0.1514 0.15 0.1541 0.1767 0.182 RANDOM 24.3474
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] -1.23 0.53 0.59 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.177 r_dihedral_angle_4_deg 14.204 r_dihedral_angle_3_deg 12.625 r_dihedral_angle_1_deg 6.384 r_scangle_it 3.623 r_scbond_it 2.498 r_angle_refined_deg 1.685 r_angle_other_deg 1.475 r_mcangle_it 1.22 r_mcbond_it 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.177 r_dihedral_angle_4_deg 14.204 r_dihedral_angle_3_deg 12.625 r_dihedral_angle_1_deg 6.384 r_scangle_it 3.623 r_scbond_it 2.498 r_angle_refined_deg 1.685 r_angle_other_deg 1.475 r_mcangle_it 1.22 r_mcbond_it 0.71 r_mcbond_other 0.232 r_chiral_restr 0.104 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1909 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 14
Software Software Software Name Purpose SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing