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Crystal structure of a prokaryotic domain of unknown function (duf849) with a tim barrel fold (bxe_c0966) from burkholderia xenovorans lb400 at 1.75 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 40.0000% 2-ethoxyethanol, 0.0500M Ca(OAc)2, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.495 α = 69.99 b = 68.275 β = 88.07 c = 83.952 γ = 72.84
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 2008-07-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97936,0.97892 SSRL BL9-2
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 1.75 29.656 97.2 0.069 0.069 6.6 2.7 115967 21.904
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) 1.75 1.8 96 0.444 0.444 1.7 2.7 8444
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 1.75 29.656 115965 5804 97.24 0.179 0.177 0.1841 0.218 0.223 RANDOM 24.44
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] -1.3 1.95 -0.71 1.19 -0.31 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.629 r_dihedral_angle_4_deg 13.596 r_dihedral_angle_3_deg 11.904 r_scangle_it 5.541 r_scbond_it 4.211 r_dihedral_angle_1_deg 4.019 r_mcangle_it 2.417 r_angle_refined_deg 1.751 r_mcbond_it 1.68 r_angle_other_deg 1.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.629 r_dihedral_angle_4_deg 13.596 r_dihedral_angle_3_deg 11.904 r_scangle_it 5.541 r_scbond_it 4.211 r_dihedral_angle_1_deg 4.019 r_mcangle_it 2.417 r_angle_refined_deg 1.751 r_mcbond_it 1.68 r_angle_other_deg 1.039 r_mcbond_other 0.321 r_symmetry_vdw_other 0.268 r_nbd_refined 0.215 r_nbd_other 0.207 r_symmetry_vdw_refined 0.197 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.185 r_xyhbond_nbd_refined 0.179 r_metal_ion_refined 0.142 r_chiral_restr 0.113 r_xyhbond_nbd_other 0.108 r_nbtor_other 0.089 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9355 Nucleic Acid Atoms Solvent Atoms 946 Heterogen Atoms 79
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