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Crystal Structure of Delta 4 mutant of EhPSAT (Phosphoserine aminotransferase of Entamoeba histolytica)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 20% PEG2000MME
100 mM Tris pH-8.5
200 mM TMAO
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.238 α = 90 b = 67.904 β = 110.93 c = 95.03 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 77.15 IMAGE PLATE RIGAKU RAXIS IV++ 2016-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.35 50 95 0.055 0.06 0.023 20.6 6.1 31390
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 68.5 0.421 0.489 0.243 0.928 3.2
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 5YB0 2.35 50 29564 1595 94.3 0.23196 0.22909 0.2293 0.28695 0.2824 RANDOM 64.222
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] 1.32 -2.98 2.27 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_dihedral_angle_3_deg 15.624 r_dihedral_angle_4_deg 13.101 r_long_range_B_refined 7.649 r_long_range_B_other 7.648 r_dihedral_angle_1_deg 6.849 r_scangle_other 5.119 r_mcangle_it 5.004 r_mcangle_other 5.004 r_scbond_it 3.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_dihedral_angle_3_deg 15.624 r_dihedral_angle_4_deg 13.101 r_long_range_B_refined 7.649 r_long_range_B_other 7.648 r_dihedral_angle_1_deg 6.849 r_scangle_other 5.119 r_mcangle_it 5.004 r_mcangle_other 5.004 r_scbond_it 3.284 r_scbond_other 3.284 r_mcbond_it 3.218 r_mcbond_other 3.217 r_angle_refined_deg 1.548 r_angle_other_deg 1.022 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5539 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling HKL-2000 data reduction DM phasing