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Crystal structure of Putative PLP-dependent aminotransferase (NP_978343.1) from Bacillus cereus ATCC 10987 at 2.19 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2000M calcium acetate, 40.0000% polyethylene glycol 300, 0.1M sodium cacodylate pH 6.5, ADDITIVE: 0.001 M PLP, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.388 α = 90 b = 90.586 β = 90 c = 131.699 γ = 90
Symmetry Space Group P 21 21 21
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 and horizontal focussing mirrors 2009-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 SSRL BL12-2
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 2.19 44.721 97.7 0.136 7.83 50328 -3 32.556
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 2.19 2.27 97.1 0.704 2.2
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 SAD THROUGHOUT 2.19 44.721 50279 2571 97.81 0.179 0.176 0.1892 0.22 0.2274 RANDOM 27.742
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] 3.31 -1.19 -2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.043 r_dihedral_angle_4_deg 17.562 r_dihedral_angle_3_deg 13.931 r_scangle_it 7.231 r_dihedral_angle_1_deg 5.578 r_scbond_it 5.125 r_mcangle_it 2.685 r_mcbond_it 1.587 r_angle_refined_deg 1.544 r_angle_other_deg 0.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.043 r_dihedral_angle_4_deg 17.562 r_dihedral_angle_3_deg 13.931 r_scangle_it 7.231 r_dihedral_angle_1_deg 5.578 r_scbond_it 5.125 r_mcangle_it 2.685 r_mcbond_it 1.587 r_angle_refined_deg 1.544 r_angle_other_deg 0.912 r_mcbond_other 0.549 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5825 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 93
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