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Crystal structure of a PLP-dependent aminotransferase (ZP_03625122.1) from Streptococcus suis 89-1591 at 2.07 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.20M lithium sulfate 2.00M ammonium sulfate, Additive: 0.001M pyridoxal 5'-phosphate (PLP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.979 α = 90 b = 83.979 β = 90 c = 176.391 γ = 120
Symmetry Space Group P 32 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 2010-07-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97920,0.97903 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 2.07 29.399 99.1 0.052 15.2 44694 -3 31.925
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 2.07 2.14 98.6 0.514 2
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 2.07 29.399 44641 2249 99.82 0.1797 0.1782 0.1837 0.2079 0.2126 RANDOM 51.4943
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] 0.82 0.41 0.82 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.811 r_dihedral_angle_4_deg 15.923 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_1_deg 4.306 r_scangle_it 3.358 r_scbond_it 2.018 r_angle_refined_deg 1.794 r_angle_other_deg 1.374 r_mcangle_it 1.173 r_mcbond_it 0.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.811 r_dihedral_angle_4_deg 15.923 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_1_deg 4.306 r_scangle_it 3.358 r_scbond_it 2.018 r_angle_refined_deg 1.794 r_angle_other_deg 1.374 r_mcangle_it 1.173 r_mcbond_it 0.624 r_mcbond_other 0.184 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5939 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 43
Software Software Software Name Purpose SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing