☰ Navigation Tabs
Crystal structure of Ap4A hydrolase (ApaH) from Pseudomonas aeruginosa in complex with ADP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 Crystal grown in 0.1M Bis-Tris pH 5.5; 0.2M MgCl2, 26-30% PEG 3350, 5% PEG200 were soaked in mother liquor containing 50 mM ADP
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.317 α = 90 b = 76.384 β = 90 c = 102.276 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 PILATUS 6M 2025-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 1.55 75.32 94.7 0.061 0.063 0.018 1 21.6 12.1 81568
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 1.55 1.58 99.4 1.495 1.56 0.439 0.8 12.3
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 (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 FREE R-VALUE 1.55 42.53 77455 4038 94.59 0.20152 0.20006 0.2095 0.22897 0.236 RANDOM 26.667
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] 2.58 -1.85 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.818 r_dihedral_angle_1_deg 6.56 r_dihedral_angle_2_deg 6.442 r_long_range_B_refined 6.135 r_long_range_B_other 6.123 r_scangle_other 5.013 r_mcangle_it 3.784 r_mcangle_other 3.784 r_scbond_it 3.426 r_scbond_other 3.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.818 r_dihedral_angle_1_deg 6.56 r_dihedral_angle_2_deg 6.442 r_long_range_B_refined 6.135 r_long_range_B_other 6.123 r_scangle_other 5.013 r_mcangle_it 3.784 r_mcangle_other 3.784 r_scbond_it 3.426 r_scbond_other 3.426 r_mcbond_it 2.741 r_mcbond_other 2.741 r_angle_refined_deg 1.762 r_angle_other_deg 0.63 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4255 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing PDB_EXTRACT data extraction