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2-aminoethylphosphonate:pyruvate aminotransferase (AEPT) native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M32
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 289 25% (w/v) PEG-3350, 0.1M Bis-Tris pH 6.5, 0.2 M Magnesium chloride hexahydrate.
Crystal Properties Matthews coefficient Solvent content 1.74 29.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.595 α = 90 b = 69.207 β = 90 c = 83.799 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2020-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 99.7 0.064 22.2 10.8 12533 53.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 0.329 1.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1M32 2.35 34.627 12493 1227 99.585 0.212 0.2096 0.2065 0.2535 0.2273 57.754
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] 1.971 -1.248 -0.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.623 r_dihedral_angle_4_deg 23.397 r_dihedral_angle_3_deg 18.78 r_lrange_it 9.153 r_dihedral_angle_1_deg 7.286 r_scangle_it 7.013 r_mcangle_it 5.415 r_scbond_it 5.073 r_mcbond_it 3.88 r_angle_refined_deg 1.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.623 r_dihedral_angle_4_deg 23.397 r_dihedral_angle_3_deg 18.78 r_lrange_it 9.153 r_dihedral_angle_1_deg 7.286 r_scangle_it 7.013 r_mcangle_it 5.415 r_scbond_it 5.073 r_mcbond_it 3.88 r_angle_refined_deg 1.401 r_nbtor_refined 0.308 r_symmetry_nbd_refined 0.257 r_symmetry_xyhbond_nbd_refined 0.241 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.198 r_chiral_restr 0.109 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2757 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing