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Crystal structure of PLP bound phosphoserine aminotransferase (PSAT) from Trichomonas vaginalis
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, HANGING DROP 289 25-30% PEG 3350 (w/v),100mM sodium acetate pH 4.5-5.0, 200mM sodium malonate, 10% glycerol (v/v)
Crystal Properties Matthews coefficient Solvent content 2.45 49.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.967 α = 90 b = 235.434 β = 90.02 c = 134.52 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 IMAGE PLATE MAR scanner 345 mm plate 2014-02-19 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 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 2.14 50 99.9 0.15 7.9 3.7 177429 32.43
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 2.14 2.23 99.8 0.44 3.3 3.6
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 1BJN 2.14 37.42 168230 9041 99.4 0.21022 0.20869 0.211 0.23905 0.2372 RANDOM 24.791
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] 0.11 6.77 -4.37 4.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.318 r_dihedral_angle_4_deg 15.758 r_dihedral_angle_3_deg 13.726 r_dihedral_angle_1_deg 6.763 r_long_range_B_refined 2.562 r_long_range_B_other 2.555 r_mcangle_it 1.381 r_mcangle_other 1.381 r_scangle_other 1.318 r_angle_refined_deg 1.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.318 r_dihedral_angle_4_deg 15.758 r_dihedral_angle_3_deg 13.726 r_dihedral_angle_1_deg 6.763 r_long_range_B_refined 2.562 r_long_range_B_other 2.555 r_mcangle_it 1.381 r_mcangle_other 1.381 r_scangle_other 1.318 r_angle_refined_deg 1.253 r_angle_other_deg 0.912 r_mcbond_it 0.813 r_mcbond_other 0.813 r_scbond_it 0.769 r_scbond_other 0.769 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 22852 Nucleic Acid Atoms Solvent Atoms 749 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling PHASER phasing