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Adenylosuccinate Synthetase from H. pylori in complex with PLP and IMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 8.5 285 85mM Tris-HCl pH 8,5
21% PEG4k
170 mM Li2SO4
15% GOL
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.897 α = 90 b = 61.124 β = 98.905 c = 119.254 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 2023-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION SUPERNOVA 1.54184
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 1.85 29.821 100 0.047 0.049 0.014 1 48 23.5 41958
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 0.24 0.261 0.102 0.991 12.7
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 1.85 29.821 41870 4135 99.752 0.17 0.1669 0.1606 0.2011 0.193 18.619
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] -0.066 0.738 0.14 -0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.421 r_dihedral_angle_3_deg 13.008 r_dihedral_angle_1_deg 7.601 r_lrange_it 6.26 r_lrange_other 6.186 r_dihedral_angle_2_deg 5.865 r_scangle_it 5.199 r_scangle_other 5.198 r_scbond_it 3.392 r_scbond_other 3.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.421 r_dihedral_angle_3_deg 13.008 r_dihedral_angle_1_deg 7.601 r_lrange_it 6.26 r_lrange_other 6.186 r_dihedral_angle_2_deg 5.865 r_scangle_it 5.199 r_scangle_other 5.198 r_scbond_it 3.392 r_scbond_other 3.391 r_mcangle_it 2.763 r_mcangle_other 2.763 r_angle_refined_deg 1.963 r_mcbond_it 1.931 r_mcbond_other 1.892 r_angle_other_deg 0.66 r_symmetry_nbd_refined 0.253 r_nbd_refined 0.224 r_symmetry_nbd_other 0.19 r_nbd_other 0.188 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.105 r_symmetry_xyhbond_nbd_refined 0.097 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3176 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement REFMAC refinement CrysalisPro data collection CrysalisPro data reduction Aimless data scaling PHASER phasing