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Crystal structure of E. coli YfbU at 2.5 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 1.6 M ammonium phosphate monobasic, 100 mM MES, pH 5.5 or 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.24 62.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 230.078 α = 90 b = 230.078 β = 90 c = 230.078 γ = 90
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 315r 2013-03-28 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-02-22 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.2146 NSLS X29A 2 SYNCHROTRON APS BEAMLINE 24-ID-C 1.0086 APS 24-ID-C 3 SYNCHROTRON NSLS BEAMLINE X29A 0.9790 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1,2,3 2.5 56 99.1 139809 138551
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2,3 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD/SIR THROUGHOUT 2.5 55.8 139809 131307 6945 99.14 0.20986 0.20789 0.2129 0.24703 0.2511 RANDOM 45.572
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_sphericity_free 22.921 r_dihedral_angle_4_deg 19.071 r_dihedral_angle_3_deg 16.296 r_sphericity_bonded 7.641 r_dihedral_angle_1_deg 4.818 r_scbond_it 3.167 r_mcangle_it 2.84 r_rigid_bond_restr 2.673 r_mcbond_it 2.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_sphericity_free 22.921 r_dihedral_angle_4_deg 19.071 r_dihedral_angle_3_deg 16.296 r_sphericity_bonded 7.641 r_dihedral_angle_1_deg 4.818 r_scbond_it 3.167 r_mcangle_it 2.84 r_rigid_bond_restr 2.673 r_mcbond_it 2.375 r_mcbond_other 2.375 r_angle_refined_deg 1.298 r_angle_other_deg 1.125 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21904 Nucleic Acid Atoms Solvent Atoms 1335 Heterogen Atoms 147
Software Software Software Name Purpose CBASS data collection SOLVE phasing MLPHARE phasing REFMAC refinement XDS data reduction XDS data scaling