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2.25 Angstrom Crystal Structure of Phosphoserine Aminotransferase (SerC) from Salmonella enterica subsp. enterica serovar Typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BJN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Protein: 7.5mGr/mL, 0.5M Sodium chloride, 0.01M TRIS-HCL pH 8.3, Screen: PACT (G1), 0.2M Sodium fluoride, 0.1M Bis Tris propane pH 7.5, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.22 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.26 α = 90 b = 82.171 β = 95.83 c = 71.925 γ = 90
Symmetry Space Group P 1 21 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 300 mm CCD Beryllium lenses 2010-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.25 30 99.9 0.077 14.5 3.8 35281 35281 -3 46.2
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) 2.25 2.29 99.2 0.477 2.3 3.2 1758
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 1BJN 2.25 29.95 33491 33491 1760 99.58 0.18833 0.18833 0.18548 0.1975 0.24235 0.2513 RANDOM 52.62
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] -1.3 -2.89 3.64 -2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.147 r_dihedral_angle_4_deg 13.151 r_dihedral_angle_3_deg 9.822 r_scangle_it 4.304 r_scbond_it 2.715 r_dihedral_angle_1_deg 2.304 r_mcangle_it 1.79 r_angle_refined_deg 1.452 r_mcbond_it 0.978 r_angle_other_deg 0.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.147 r_dihedral_angle_4_deg 13.151 r_dihedral_angle_3_deg 9.822 r_scangle_it 4.304 r_scbond_it 2.715 r_dihedral_angle_1_deg 2.304 r_mcangle_it 1.79 r_angle_refined_deg 1.452 r_mcbond_it 0.978 r_angle_other_deg 0.878 r_mcbond_other 0.24 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5114 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 2
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling