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Crystal Structure of Wild Type Phosphoserine aminotransferase (PSAT) from E. histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289.15 25-30% PEG 3350 (w/v),
100 mM Tris pH 6.5,
200mM sodium formate,
5 % glycerol (v/v)
Crystal Properties Matthews coefficient Solvent content 2.37 43.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.446 α = 62.85 b = 134.073 β = 88.58 c = 139.064 γ = 74.92
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77.15 CCD MAR CCD 165 mm 2011-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
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 2.94 50.15 94.2 0.083 0.051 14.911 3.7 76771
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 3 3.05 85.8 0.881 1.9
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 1BT4 2.94 50.15 73001 3764 87.9 0.267 0.265 0.2577 0.301 0.2969 RANDOM 76.93
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] 9.03 -37.97 23.05 -6.13 8.3 -2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.526 r_dihedral_angle_3_deg 18.187 r_dihedral_angle_4_deg 11.811 r_dihedral_angle_1_deg 8.333 r_angle_refined_deg 1.553 r_angle_other_deg 1.091 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_bond_other_d 0.008 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.526 r_dihedral_angle_3_deg 18.187 r_dihedral_angle_4_deg 11.811 r_dihedral_angle_1_deg 8.333 r_angle_refined_deg 1.553 r_angle_other_deg 1.091 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_bond_other_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27082 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 165
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection PDB_EXTRACT data extraction HKL-2000 data reduction