☰ Navigation Tabs
X-ray structure of the lysozyme derivative of tetrakis(acetato)chlorido diruthenium(II,III) complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J1A PDb 4J1A without solvent and ligands
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 Crystals of HEWL in the presence of the diruthernium compound (1:10 ratio) suitable for X-ray diffraction were grown at 293 K using the hanging drop vapour diffusion method, 1.0-1.2 mol L-1 NaCl as a precipitating agent in 0.050 mol L-1 acetate buffer at pH 4.2 and protein concentration 15 mg mL-1. , VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 1.98 38.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.292 α = 90 b = 78.292 β = 90 c = 37.119 γ = 90
Symmetry Space Group P 43 21 2
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+ M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 2.15 55.36 99 0.133 11.8 6686 6686
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 100 0.535 6 12.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDb 4J1A without solvent and ligands 2.15 55.36 6598 6290 308 98.74 0.211 0.19172 0.1888 0.1881 0.25431 0.2555 RANDOM 30.496
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] 0.58 0.58 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.701 r_dihedral_angle_4_deg 19.932 r_dihedral_angle_3_deg 15.638 r_dihedral_angle_1_deg 6.59 r_scangle_it 4.114 r_scbond_it 2.739 r_angle_refined_deg 1.762 r_mcangle_it 1.594 r_mcbond_it 0.948 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.701 r_dihedral_angle_4_deg 19.932 r_dihedral_angle_3_deg 15.638 r_dihedral_angle_1_deg 6.59 r_scangle_it 4.114 r_scbond_it 2.739 r_angle_refined_deg 1.762 r_mcangle_it 1.594 r_mcbond_it 0.948 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement CNS refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing