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Crystal Structure of Asparagine Synthetase from Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LNS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 Ammonium sulfate, Bis tris pH 5.6, 30% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.252 α = 90 b = 149.848 β = 90 c = 170.507 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 4M 2022-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.918 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.1 85.25 97.7 0.992 7.7 3 61162
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.44 0.802
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.38 85.25 61140 3013 97.237 0.18 0.1777 0.1856 0.2254 0.1859 30.771
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] -1.371 3.688 -2.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.037 r_dihedral_angle_6_deg 15.779 r_dihedral_angle_2_deg 10.844 r_lrange_it 7.301 r_lrange_other 7.301 r_dihedral_angle_1_deg 6.556 r_scangle_it 4.207 r_scangle_other 4.207 r_mcangle_it 2.855 r_mcangle_other 2.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.037 r_dihedral_angle_6_deg 15.779 r_dihedral_angle_2_deg 10.844 r_lrange_it 7.301 r_lrange_other 7.301 r_dihedral_angle_1_deg 6.556 r_scangle_it 4.207 r_scangle_other 4.207 r_mcangle_it 2.855 r_mcangle_other 2.855 r_scbond_it 2.608 r_scbond_other 2.608 r_mcbond_it 1.785 r_mcbond_other 1.785 r_angle_refined_deg 1.406 r_angle_other_deg 0.455 r_symmetry_nbd_refined 0.327 r_nbd_other 0.309 r_symmetry_xyhbond_nbd_refined 0.306 r_symmetry_nbd_other 0.214 r_nbd_refined 0.213 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_other 0.132 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10834 Nucleic Acid Atoms Solvent Atoms 756 Heterogen Atoms 214
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing