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Crystal structure of Putative serine-pyruvate aminotransferase (YP_263484.1) from PSYCHROBACTER ARCTICUM 273-4 at 2.20 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 25.0000% polyethylene glycol 4000, 0.2000M ammonium sulfate, 0.1M sodium acetate pH 4.6, Additive: 0.001M pyridoxal-5'-phospate (PLP), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.645 α = 90 b = 98.352 β = 90 c = 121.072 γ = 90
Symmetry Space Group C 2 2 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 MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.91162,0.97956,0.97938 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 29.867 99.8 0.125 0.125 8.8 3.7 19035 32.162
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 99.9 0.652 0.652 1.2 3.7 1388
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 2.2 29.867 19024 983 99.77 0.169 0.167 0.1818 0.21 0.222 RANDOM 18.099
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] -1.67 1.8 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.33 r_dihedral_angle_4_deg 17.055 r_dihedral_angle_3_deg 14.128 r_scangle_it 5.506 r_dihedral_angle_1_deg 4.756 r_scbond_it 3.935 r_mcangle_it 2.1 r_angle_refined_deg 1.543 r_angle_other_deg 1.139 r_mcbond_it 1.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.33 r_dihedral_angle_4_deg 17.055 r_dihedral_angle_3_deg 14.128 r_scangle_it 5.506 r_dihedral_angle_1_deg 4.756 r_scbond_it 3.935 r_mcangle_it 2.1 r_angle_refined_deg 1.543 r_angle_other_deg 1.139 r_mcbond_it 1.069 r_mcbond_other 0.204 r_chiral_restr 0.094 r_bond_refined_d 0.016 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 2847 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing