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Crystal structure and substrate specificity of a thermophilic archaeal serine : pyruvate aminotransferase from Sulfolobus solfataricus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BKW PDB ENTRY 2BKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 5 MG/ML PROTEIN, 50 MM TRIS HCL PH 8.5 AND 15% POLYETHYLENE GLYCOL (PEG) 400.
Crystal Properties Matthews coefficient Solvent content 2.35 47.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.43 α = 90 b = 54.97 β = 111.27 c = 101.81 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 CCD ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
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 1.75 24 95 0.05 8.7 2.7 76065 1.6 39.7
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 1.75 1.84 76.5 0.39 1.6 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 PDB ENTRY 2BKW 1.75 94.87 76065 4029 93.7 0.21827 0.21604 0.2138 0.2596 0.258 RANDOM 39.366
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] -2.07 -0.92 3.5 -2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.054 r_dihedral_angle_4_deg 17.655 r_dihedral_angle_3_deg 16.424 r_dihedral_angle_1_deg 5.075 r_angle_refined_deg 1.291 r_chiral_restr 0.085 r_bond_refined_d 0.012 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 35.054 r_dihedral_angle_4_deg 17.655 r_dihedral_angle_3_deg 16.424 r_dihedral_angle_1_deg 5.075 r_angle_refined_deg 1.291 r_chiral_restr 0.085 r_bond_refined_d 0.012 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_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 5808 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling BALBES phasing