8BPJ

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-p-FPhF)(O2CCH3)3] (Structure 1)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429320% ethylene glycol, 0.1 M sodium acetate buffer at pH 4.0, 0.6 M sodium nitrate
Crystal Properties
Matthews coefficientSolvent content
1.9536.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.48α = 90
b = 77.48β = 90
c = 37.27γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.3854.7999.90.0470.9921.810.323817
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)
11.381.40.9350.8332.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE193L1.3854.7923817119799.9330.1920.19010.230624.069
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]
-0.049-0.0490.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.303
r_dihedral_angle_4_deg20.462
r_dihedral_angle_3_deg16.08
r_dihedral_angle_1_deg6.64
r_lrange_it6.341
r_lrange_other6.27
r_scangle_it4.813
r_scangle_other4.795
r_scbond_it3.194
r_scbond_other3.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.303
r_dihedral_angle_4_deg20.462
r_dihedral_angle_3_deg16.08
r_dihedral_angle_1_deg6.64
r_lrange_it6.341
r_lrange_other6.27
r_scangle_it4.813
r_scangle_other4.795
r_scbond_it3.194
r_scbond_other3.14
r_mcangle_it2.908
r_mcangle_other2.908
r_mcbond_it2.079
r_mcbond_other2.075
r_angle_refined_deg1.921
r_angle_other_deg1.577
r_symmetry_xyhbond_nbd_refined0.258
r_nbd_refined0.234
r_nbd_other0.227
r_xyhbond_nbd_refined0.219
r_symmetry_nbd_other0.198
r_symmetry_nbd_refined0.189
r_nbtor_refined0.173
r_symmetry_xyhbond_nbd_other0.154
r_metal_ion_refined0.136
r_chiral_restr0.1
r_symmetry_nbtor_other0.086
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing