6PL9

Adduct formed after 1 month in the reaction of dichlorido(1,3-dimethylbenzimidaz ol-2-ylidene)(eta5-pentamethylcyclopentadienyl)rhodium(III) with HEWL


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP297Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Rh(III)(Cp*)(1,3-dimethylbenzimidazol-2-ylidene)(Cl)2 (1.09 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
2.1342.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.425α = 90
b = 80.425β = 90
c = 37.794γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2017-10-14MSINGLE 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
11.237.791000.0630.0660.0180.99922.514.139348
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)
11.21.221003.7743.941.1180.31212.2

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 REPLACEMENTTHROUGHOUT4NHI1.235.9937290199899.990.17350.1720.2027RANDOM17.316
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]
1.431.43-2.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.496
r_dihedral_angle_4_deg20.883
r_dihedral_angle_3_deg13.54
r_dihedral_angle_1_deg6.726
r_angle_refined_deg1.664
r_angle_other_deg1.433
r_rigid_bond_restr1.113
r_chiral_restr0.076
r_bond_refined_d0.005
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.496
r_dihedral_angle_4_deg20.883
r_dihedral_angle_3_deg13.54
r_dihedral_angle_1_deg6.726
r_angle_refined_deg1.664
r_angle_other_deg1.433
r_rigid_bond_restr1.113
r_chiral_restr0.076
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms37

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction