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Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_348457.1) from Clostridium acetobutylicum at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.43 277 0.9500M sodium citrate, 0.1M sodium cacodylate pH 6.43, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.83 α = 90 b = 186.62 β = 103.06 c = 93.71 γ = 90
Symmetry Space Group P 1 21 1
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 2008-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 30.029 97 0.056 9.52 3.52 131295 -3 26.888
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 2.07 90 0.346 1.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2 30.029 131250 6601 99.26 0.147 0.145 0.187 0.1993 RANDOM 36.557
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] 1.17 1.51 -0.54 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.833 r_dihedral_angle_4_deg 15.796 r_dihedral_angle_3_deg 12.549 r_scangle_it 7.692 r_scbond_it 5.847 r_dihedral_angle_1_deg 4.772 r_mcangle_it 3.078 r_mcbond_it 1.855 r_angle_refined_deg 1.633 r_angle_other_deg 0.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.833 r_dihedral_angle_4_deg 15.796 r_dihedral_angle_3_deg 12.549 r_scangle_it 7.692 r_scbond_it 5.847 r_dihedral_angle_1_deg 4.772 r_mcangle_it 3.078 r_mcbond_it 1.855 r_angle_refined_deg 1.633 r_angle_other_deg 0.995 r_mcbond_other 0.541 r_symmetry_vdw_other 0.31 r_nbd_refined 0.229 r_nbd_other 0.196 r_symmetry_hbond_refined 0.193 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.184 r_metal_ion_refined 0.135 r_chiral_restr 0.1 r_nbtor_other 0.093 r_symmetry_vdw_refined 0.093 r_xyhbond_nbd_other 0.043 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12909 Nucleic Acid Atoms Solvent Atoms 865 Heterogen Atoms 76
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