5OB6

X-ray structure of the adduct formed upon reaction of lysozyme with the compound fac-[RuII(CO)3Cl2(N3-IM), IM=imidazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 193L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2981.1 M NaCl, 0.1 M sodium acetate at pH 4.0-4.4. Adduct was prepared by mixing the protein with the metallodrug in a 1:10 molar ratio for 24 h at room temperature before crystallization trials.
Crystal Properties
Matthews coefficientSolvent content
2.0339.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.776α = 90
b = 79.776β = 90
c = 36.637γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944mirrors2014-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.8856.4198.20.09113.35.19931
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.921000.5972.73.2

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 REPLACEMENTTHROUGHOUT193L1.8856.41942847798.130.178570.175330.24189RANDOM32.201
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]
-0.22-0.220.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.675
r_dihedral_angle_4_deg19.826
r_dihedral_angle_3_deg15.937
r_long_range_B_other6.706
r_long_range_B_refined6.687
r_dihedral_angle_1_deg6.661
r_scangle_other4.782
r_scbond_it3.414
r_mcangle_other3.366
r_mcangle_it3.347
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.675
r_dihedral_angle_4_deg19.826
r_dihedral_angle_3_deg15.937
r_long_range_B_other6.706
r_long_range_B_refined6.687
r_dihedral_angle_1_deg6.661
r_scangle_other4.782
r_scbond_it3.414
r_mcangle_other3.366
r_mcangle_it3.347
r_scbond_other3.339
r_mcbond_it2.503
r_mcbond_other2.468
r_angle_refined_deg1.932
r_angle_other_deg1.152
r_chiral_restr0.125
r_bond_refined_d0.021
r_gen_planes_refined0.008
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 Atoms147
Heterogen Atoms35

Software

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