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Structure of the cystathionine beta-synthase pair domain of the putative Mg2+ transporter SO5017 from Shewanella oneidensis MR-1.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 295 PEG3350 25%,di-Na-Tartrate 0.2M,Tris0.1M pH8.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.92 57.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.596 α = 90 b = 103.596 β = 90 c = 134.302 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 315r MIRROR 2009-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9791 APS 19-ID
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 2.4 50 99.9 0.093 0.093 57.071 18.5 10867 10867 -3 61.8
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 2.4 2.44 98.2 0.878 0.878 3.6 18.3 537
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 (All) 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 THROUGHOUT 2.41 50 10835 10835 517 99.59 0.191 0.191 0.19 0.196 0.228 0.2305 RANDOM 37.37
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] -1.86 -0.93 -1.86 2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.858 r_dihedral_angle_4_deg 21.58 r_dihedral_angle_3_deg 16.647 r_dihedral_angle_1_deg 5.789 r_scangle_it 4.147 r_scbond_it 2.603 r_angle_refined_deg 1.453 r_mcangle_it 1.414 r_angle_other_deg 0.906 r_mcbond_it 0.695
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.858 r_dihedral_angle_4_deg 21.58 r_dihedral_angle_3_deg 16.647 r_dihedral_angle_1_deg 5.789 r_scangle_it 4.147 r_scbond_it 2.603 r_angle_refined_deg 1.453 r_mcangle_it 1.414 r_angle_other_deg 0.906 r_mcbond_it 0.695 r_mcbond_other 0.127 r_chiral_restr 0.08 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1364 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 2
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing MLPHARE phasing DM model building SHELXD phasing ARP/wARP model building CCP4 model building REFMAC refinement Coot model building HKL-3000 data reduction HKL-2000 data scaling DM phasing CCP4 phasing