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Crystal structure of Serine acetyltransferase from Vibrio cholerae O1 biovar El Tor N16961
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T3D PDB ENTRY 1t3d
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 273 10% Peg4000, 20% Glycerol, 0.03M MgCl2,CaCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.18 43.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.04 α = 90 b = 75.04 β = 89.04 c = 73.43 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 IMAGE PLATE MAR scanner 345 mm plate 2012-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.953 ESRF BM14
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 2.17 50 97.4 0.104 7.7 40442 38412 -3
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 2.17 2.21 87.4 0.356 5.06 6.6 1796
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1t3d 2.17 37.52 38412 2027 97.26 0.17957 0.17742 0.1738 0.21998 0.2163 RANDOM 29.182
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] -0.24 0.32 -0.01 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.018 r_dihedral_angle_4_deg 16.264 r_dihedral_angle_3_deg 14.832 r_dihedral_angle_1_deg 6.188 r_angle_refined_deg 1.373 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.018 r_dihedral_angle_4_deg 16.264 r_dihedral_angle_3_deg 14.832 r_dihedral_angle_1_deg 6.188 r_angle_refined_deg 1.373 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5817 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 58
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling