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Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (YP_165505.1) from Silicibacter pomeroyi DSS-3 at 1.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.6 277 0.4000M magnesium chloride, 18.0000% polyethylene glycol 8000, 0.1M TRIS pH 8.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.409 α = 90 b = 136.411 β = 118 c = 50.548 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) 2009-06-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97917,0.97862 SSRL BL11-1
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 1.6 27.277 99.3 0.074 0.074 9.3 2.6 78581 16.453
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 1.6 1.64 98.4 0.417 0.417 2 2.5 5758
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 1.6 27.277 78539 3949 99.19 0.158 0.156 0.1654 0.187 0.193 RANDOM 13.92
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] 1.36 0.53 -0.64 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.849 r_dihedral_angle_4_deg 14.015 r_dihedral_angle_3_deg 11.222 r_dihedral_angle_1_deg 4.51 r_scangle_it 2.598 r_mcangle_it 2.004 r_scbond_it 1.719 r_angle_refined_deg 1.716 r_mcbond_it 1.332 r_angle_other_deg 1.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.849 r_dihedral_angle_4_deg 14.015 r_dihedral_angle_3_deg 11.222 r_dihedral_angle_1_deg 4.51 r_scangle_it 2.598 r_mcangle_it 2.004 r_scbond_it 1.719 r_angle_refined_deg 1.716 r_mcbond_it 1.332 r_angle_other_deg 1.041 r_mcbond_other 0.41 r_chiral_restr 0.085 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4532 Nucleic Acid Atoms Solvent Atoms 701 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing