8PH8

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(DPhF)2(O2CCH3)2] in condition A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.8 M succinic acid at pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.0138.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.89α = 90
b = 76.89β = 90
c = 37.89γ = 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
11.2954.3799.70.0740.99921.220.837185
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)
11.291.311.140.7632.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE1.2954.33629187144699.9550.1580.15630.187318.008
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]
-0.059-0.0590.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.328
r_dihedral_angle_4_deg23.915
r_dihedral_angle_3_deg11.623
r_dihedral_angle_1_deg6.626
r_lrange_it5.661
r_lrange_other5.179
r_scangle_it3.468
r_scangle_other3.466
r_scbond_other2.248
r_scbond_it2.247
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.328
r_dihedral_angle_4_deg23.915
r_dihedral_angle_3_deg11.623
r_dihedral_angle_1_deg6.626
r_lrange_it5.661
r_lrange_other5.179
r_scangle_it3.468
r_scangle_other3.466
r_scbond_other2.248
r_scbond_it2.247
r_mcangle_other2.203
r_mcangle_it2.176
r_angle_refined_deg1.922
r_angle_other_deg1.642
r_mcbond_it1.458
r_mcbond_other1.391
r_symmetry_nbd_refined0.272
r_xyhbond_nbd_refined0.264
r_nbd_other0.233
r_nbd_refined0.227
r_nbtor_refined0.189
r_symmetry_nbd_other0.188
r_symmetry_xyhbond_nbd_refined0.155
r_metal_ion_refined0.112
r_chiral_restr0.104
r_symmetry_nbtor_other0.085
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 Atoms177
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing