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CRYSTAL STRUCTURE OF A PUTATIVE PLP-DEPENDENT AMINOTRANSFERASE (LBUL_1103) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.61 A RESOLUTION
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2M calcium acetate, 40.0% polyethylene glycol 300, 0.1M sodium cacodylate pH 6.5, Additive - 0.001M pyridoxal 5'-phosphate (PLP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K, NANODROP'
Crystal Properties Matthews coefficient Solvent content 2.06 40.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.8 α = 90 b = 94.8 β = 127.13 c = 84.602 γ = 90
Symmetry Space Group C 1 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 mirror (vertical focusing) 2008-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 1.61 38.778 98.5 0.07 9.47 3.71 93024 -3 18.602
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 1.61 1.67 99.6 0.605 2.32
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 SAD THROUGHOUT 1.61 38.778 93023 4663 98.86 0.146 0.144 0.1605 0.175 0.1846 RANDOM 16.011
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] -0.55 -0.14 -0.01 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.964 r_dihedral_angle_4_deg 19.686 r_dihedral_angle_3_deg 12.167 r_scangle_it 7.089 r_dihedral_angle_1_deg 5.958 r_scbond_it 4.898 r_mcangle_it 2.763 r_mcbond_it 1.824 r_angle_refined_deg 1.742 r_angle_other_deg 1.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.964 r_dihedral_angle_4_deg 19.686 r_dihedral_angle_3_deg 12.167 r_scangle_it 7.089 r_dihedral_angle_1_deg 5.958 r_scbond_it 4.898 r_mcangle_it 2.763 r_mcbond_it 1.824 r_angle_refined_deg 1.742 r_angle_other_deg 1.088 r_mcbond_other 0.564 r_chiral_restr 0.107 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5988 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 60
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