8BPH

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


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
Crystal Properties
Matthews coefficientSolvent content
1.9737.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.19α = 90
b = 77.19β = 90
c = 37.83γ = 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 11.2C1.00ELETTRA11.2C

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
11.0738.60396.80.042133.819.3949875
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)
11.071.090.8090.832.8

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-VALUE193L1.0738.60348803242195.8760.1870.18570.209115.021
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]
-0.059-0.0590.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.714
r_dihedral_angle_4_deg16.766
r_dihedral_angle_3_deg15.227
r_lrange_it7.999
r_lrange_other7.63
r_dihedral_angle_1_deg6.821
r_scangle_other3.709
r_scangle_it3.647
r_scbond_other2.381
r_scbond_it2.371
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.714
r_dihedral_angle_4_deg16.766
r_dihedral_angle_3_deg15.227
r_lrange_it7.999
r_lrange_other7.63
r_dihedral_angle_1_deg6.821
r_scangle_other3.709
r_scangle_it3.647
r_scbond_other2.381
r_scbond_it2.371
r_angle_refined_deg2.065
r_mcangle_other2.064
r_mcangle_it2.047
r_angle_other_deg1.686
r_mcbond_it1.364
r_mcbond_other1.33
r_nbd_refined0.274
r_nbd_other0.248
r_xyhbond_nbd_refined0.242
r_symmetry_nbd_refined0.239
r_symmetry_nbd_other0.224
r_symmetry_xyhbond_nbd_refined0.219
r_nbtor_refined0.184
r_chiral_restr0.121
r_symmetry_nbtor_other0.091
r_symmetry_xyhbond_nbd_other0.08
r_bond_refined_d0.016
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms992
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing