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Crystal structure of a putative plp-dependent beta-cystathionase (aecd, dip1736) from corynebacterium diphtheriae at 1.99 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2000M MgCl2, 10.0000% PEG-3000, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.51 64.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.18 α = 90 b = 69.18 β = 90 c = 215.46 γ = 120
Symmetry Space Group P 31 2 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 2008-08-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97934,0.97922 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 1.99 29.961 99.1 0.061 10.77 47285 -3 30.512
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 1.91 1.98 98.5 0.73 1.5
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 1.99 29.961 41858 2140 99.43 0.149 0.147 0.1589 0.175 0.1845 RANDOM 43.667
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] 2.28 1.14 2.28 -3.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.315 r_dihedral_angle_4_deg 12.891 r_dihedral_angle_3_deg 11.185 r_scangle_it 7.027 r_scbond_it 5.015 r_dihedral_angle_1_deg 4.65 r_mcangle_it 2.525 r_mcbond_it 1.579 r_angle_refined_deg 1.471 r_angle_other_deg 0.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.315 r_dihedral_angle_4_deg 12.891 r_dihedral_angle_3_deg 11.185 r_scangle_it 7.027 r_scbond_it 5.015 r_dihedral_angle_1_deg 4.65 r_mcangle_it 2.525 r_mcbond_it 1.579 r_angle_refined_deg 1.471 r_angle_other_deg 0.967 r_mcbond_other 0.48 r_symmetry_vdw_other 0.272 r_symmetry_hbond_refined 0.248 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.213 r_metal_ion_refined 0.198 r_nbd_other 0.196 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.095 r_nbtor_other 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2950 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 42
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