8BQM

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-p-FPhF)(O2CCH3)3] (Structure 4)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42931.1 M sodium chloride, 0.1 M sodium acetate buffer pH 4.0
Crystal Properties
Matthews coefficientSolvent content
1.9737.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.74α = 90
b = 77.74β = 90
c = 37.38γ = 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
11.1754.9799.60.04137.821.639386
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.171.190.742.3

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-VALUE193L1.1754.9739063199699.6580.1990.19730.22518.806
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]
0.0270.027-0.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.356
r_dihedral_angle_4_deg17.098
r_dihedral_angle_3_deg14.577
r_dihedral_angle_1_deg6.535
r_lrange_it5.027
r_lrange_other4.94
r_scangle_other3.75
r_scangle_it3.713
r_scbond_other2.429
r_scbond_it2.413
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.356
r_dihedral_angle_4_deg17.098
r_dihedral_angle_3_deg14.577
r_dihedral_angle_1_deg6.535
r_lrange_it5.027
r_lrange_other4.94
r_scangle_other3.75
r_scangle_it3.713
r_scbond_other2.429
r_scbond_it2.413
r_mcangle_other2.157
r_mcangle_it2.156
r_angle_refined_deg2.093
r_angle_other_deg1.62
r_mcbond_it1.52
r_mcbond_other1.497
r_symmetry_xyhbond_nbd_refined0.255
r_nbd_refined0.24
r_nbd_other0.203
r_symmetry_nbd_other0.2
r_xyhbond_nbd_refined0.183
r_nbtor_refined0.176
r_symmetry_nbd_refined0.166
r_chiral_restr0.113
r_symmetry_nbtor_other0.094
r_metal_ion_refined0.081
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_ext_dist_refined_d0.007
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing