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Adenylosuccinate Synthetase from H. pylori in complex with IMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M9D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.35 294 PEG 3350, ammonium sulphate, Bis-Tris Propane
Crystal Properties Matthews coefficient Solvent content 2.74 55.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.105 α = 90 b = 61.326 β = 98.417 c = 119.636 γ = 90
Symmetry Space Group I 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 AGILENT ATLAS CCD 2021-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION SUPERNOVA 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 23.51 99.9 0.053 0.055 0.015 1 38.7 13.6 33613 16.55
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 2.05 100 0.987 9.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4m9d 2 23.45 1.91 33592 1679 99.93 0.1789 0.1773 0.1768 0.21 0.2101 17.88
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.3126 f_angle_d 0.8855 f_chiral_restr 0.0573 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3196 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement PHENIX refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing