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Crystal structure of a putative metal-dependent phosphoesterase (bad_1165) from bifidobacterium adolescentis atcc 15703 at 2.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 0.0200M CaCl2, 30.0000% MPD, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.46 α = 90 b = 102.46 β = 90 c = 54.17 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 2.4 29.579 99.7 0.119 12857 -3 36.482
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 2.4 2.49 99.3 0.525 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.4 29.579 12839 626 99.89 0.152 0.149 0.207 0.2125 RANDOM 24.211
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] 0.95 0.48 0.95 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_4_deg 20.646 r_dihedral_angle_3_deg 15.435 r_scangle_it 7.63 r_dihedral_angle_1_deg 5.906 r_scbond_it 5.557 r_mcangle_it 3.087 r_mcbond_it 2.122 r_angle_refined_deg 1.47 r_angle_other_deg 0.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.641 r_dihedral_angle_4_deg 20.646 r_dihedral_angle_3_deg 15.435 r_scangle_it 7.63 r_dihedral_angle_1_deg 5.906 r_scbond_it 5.557 r_mcangle_it 3.087 r_mcbond_it 2.122 r_angle_refined_deg 1.47 r_angle_other_deg 0.943 r_mcbond_other 0.436 r_nbd_refined 0.2 r_nbd_other 0.199 r_xyhbond_nbd_refined 0.181 r_symmetry_vdw_other 0.18 r_symmetry_vdw_refined 0.172 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.128 r_nbtor_other 0.088 r_chiral_restr 0.075 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2154 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing