6GOI

X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated triphenylphosphonium cation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DPX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.429320% ethylene glycol 0.6 M sodium nitrate 0.1 M sodium acetate pH 4.4
Crystal Properties
Matthews coefficientSolvent content
2.0138.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.443α = 90
b = 78.443β = 90
c = 37.385γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442018-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.9955.4799.60.10712.14.88433
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)RedundancyNumber Unique Reflections (All)
11.992.0299.50.5690.8271.74

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 REPLACEMENTTHROUGHOUT1dpx1.9955.47799441399.730.170270.166510.24184RANDOM25.859
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]
-0.19-0.190.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.877
r_dihedral_angle_4_deg21.535
r_dihedral_angle_3_deg13.637
r_long_range_B_other6.889
r_long_range_B_refined6.888
r_dihedral_angle_1_deg6.582
r_scangle_other4.644
r_scbond_it3.035
r_scbond_other3.034
r_mcangle_it2.446
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.877
r_dihedral_angle_4_deg21.535
r_dihedral_angle_3_deg13.637
r_long_range_B_other6.889
r_long_range_B_refined6.888
r_dihedral_angle_1_deg6.582
r_scangle_other4.644
r_scbond_it3.035
r_scbond_other3.034
r_mcangle_it2.446
r_mcangle_other2.446
r_angle_refined_deg1.744
r_mcbond_it1.693
r_mcbond_other1.688
r_angle_other_deg1.084
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing