☰ Navigation Tabs
Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa complexed with adenine, K+ and Zn2+ cations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 50 mM KH2PO4, 20% (w/v) PEG8000, 2 mM 2'-deoxyadenosine
Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.839 α = 90 b = 99.614 β = 101.97 c = 111.825 γ = 90
Symmetry Space Group C 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 RAYONIX MX-225 2014-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.8950 BESSY 14.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 25 99.9 0.078 17.6 4.2 182928 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81
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 (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 THROUGHOUT 6F3P 1.75 25 181035 1806 99.69 0.14003 0.13976 0.153 0.16712 0.1787 RANDOM 25.543
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] 0.03 -0.08 0.24 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.562 r_dihedral_angle_4_deg 14.423 r_dihedral_angle_3_deg 12.988 r_dihedral_angle_1_deg 6.351 r_long_range_B_refined 4.235 r_long_range_B_other 4.066 r_scangle_other 2.501 r_angle_refined_deg 1.657 r_scbond_it 1.631 r_scbond_other 1.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.562 r_dihedral_angle_4_deg 14.423 r_dihedral_angle_3_deg 12.988 r_dihedral_angle_1_deg 6.351 r_long_range_B_refined 4.235 r_long_range_B_other 4.066 r_scangle_other 2.501 r_angle_refined_deg 1.657 r_scbond_it 1.631 r_scbond_other 1.631 r_mcangle_it 1.494 r_mcangle_other 1.494 r_mcbond_it 1.052 r_mcbond_other 1.052 r_angle_other_deg 0.983 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 14196 Nucleic Acid Atoms Solvent Atoms 1616 Heterogen Atoms 268
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing ARP/wARP model building