6BO2

Adducts formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimidazol-2-ylidene)(eta6-p-cymene)ruthenium(II) with HEWL


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NHI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.7294Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Ru(II)(cymene)(1,3-dimethylbenzimidazol-2-ylidene)(chlorido)2 (1.04 mg, 1 mg/mL) soak occurred in 0.8 M sodium nitrate and 0.1 M sodium acetate pH 4.7
Crystal Properties
Matthews coefficientSolvent content
238.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.762α = 90
b = 78.762β = 90
c = 36.928γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2017-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4855.691000.070.0730.0210.99920.711.819993
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)RedundancyNumber Unique Reflections (All)
11.481.599.33.0793.2320.9650.30310.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4NHI1.4855.691898694499.990.18790.18550.2329RANDOM29.541
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]
-1.34-1.342.68
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.936
r_dihedral_angle_2_deg38.209
r_dihedral_angle_4_deg18.666
r_sphericity_bonded17.517
r_dihedral_angle_3_deg14.98
r_dihedral_angle_1_deg6.409
r_rigid_bond_restr1.871
r_angle_refined_deg1.504
r_angle_other_deg1.034
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.936
r_dihedral_angle_2_deg38.209
r_dihedral_angle_4_deg18.666
r_sphericity_bonded17.517
r_dihedral_angle_3_deg14.98
r_dihedral_angle_1_deg6.409
r_rigid_bond_restr1.871
r_angle_refined_deg1.504
r_angle_other_deg1.034
r_chiral_restr0.095
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms31

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building