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Crystal structure of a putative metal-dependent phosphoesterase (BAD_1165) from bifidobacterium adolescentis atcc 15703 at 1.94 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.71 277 24.0000% 2-methyl-2,4-pentanediol, 0.0200M calcium acetate, 0.1M sodium acetate pH 4.71, 0.005 M adenosine 5'-monophosphate, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.57 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.341 α = 90 b = 103.341 β = 90 c = 54.744 γ = 120
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 315 2010-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
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 1.94 44.748 99.6 0.167 12.54 24784 -3 18.988
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 1.94 2.01 97.7 0.799 2.6
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 MOLECULAR REPLACEMENT THROUGHOUT 1.94 44.748 24761 1241 99.62 0.1613 0.1597 0.1659 0.1916 0.1956 RANDOM 23.7813
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] 0.41 0.2 0.41 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.8 r_dihedral_angle_4_deg 20.717 r_dihedral_angle_3_deg 14.018 r_scangle_it 7.989 r_dihedral_angle_1_deg 6.107 r_scbond_it 5.726 r_mcangle_it 3.245 r_mcbond_it 1.973 r_angle_refined_deg 1.607 r_angle_other_deg 1.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.8 r_dihedral_angle_4_deg 20.717 r_dihedral_angle_3_deg 14.018 r_scangle_it 7.989 r_dihedral_angle_1_deg 6.107 r_scbond_it 5.726 r_mcangle_it 3.245 r_mcbond_it 1.973 r_angle_refined_deg 1.607 r_angle_other_deg 1.176 r_mcbond_other 0.593 r_chiral_restr 0.132 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2151 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction