☰ Navigation Tabs
X-ray structure of the adduct formed upon reaction of bovine pancreatic ribonuclease with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 293 20% PEG4000
10 mM sodium citrate buffer pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.18 43.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.282 α = 90 b = 32.805 β = 90.61 c = 72.661 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 RIGAKU SATURN 944 2018-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.65 72.66 91.1 0.09 12.1 2.5 6649
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 79.2 0.391 0.834 1.6 2.3
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 1fs3 2.65 72.66 6196 309 91.22 0.19066 0.18722 0.1922 0.25476 0.2499 RANDOM 48.959
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] -1.2 1.35 1.43 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.104 r_dihedral_angle_3_deg 16.515 r_dihedral_angle_4_deg 12.549 r_long_range_B_refined 8.045 r_long_range_B_other 8.043 r_dihedral_angle_1_deg 7.087 r_mcangle_it 5.287 r_mcangle_other 5.286 r_scangle_other 5.062 r_mcbond_it 3.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.104 r_dihedral_angle_3_deg 16.515 r_dihedral_angle_4_deg 12.549 r_long_range_B_refined 8.045 r_long_range_B_other 8.043 r_dihedral_angle_1_deg 7.087 r_mcangle_it 5.287 r_mcangle_other 5.286 r_scangle_other 5.062 r_mcbond_it 3.301 r_mcbond_other 3.301 r_scbond_it 3.087 r_scbond_other 3.086 r_angle_refined_deg 1.637 r_angle_other_deg 1.205 r_chiral_restr 0.079 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 r_gen_planes_other 0.007 r_bond_other_d 0.005 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 1902 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing