8PH7

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(DPhF)(O2CCH3)3] 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 = 77.67α = 90
b = 77.67β = 90
c = 38.28γ = 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
11.40654.92199.40.1640.99813.319.314799
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)
11.4061.532.7640.8672

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-VALUE1.40654.9211479974263.3850.2290.22640.266424.732
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]
-0.295-0.2950.589
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.923
r_dihedral_angle_6_deg15.551
r_lrange_it8.612
r_lrange_other8.585
r_dihedral_angle_2_deg8.498
r_dihedral_angle_1_deg7.113
r_scangle_it4.998
r_scangle_other4.995
r_mcangle_other3.467
r_mcangle_it3.464
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.923
r_dihedral_angle_6_deg15.551
r_lrange_it8.612
r_lrange_other8.585
r_dihedral_angle_2_deg8.498
r_dihedral_angle_1_deg7.113
r_scangle_it4.998
r_scangle_other4.995
r_mcangle_other3.467
r_mcangle_it3.464
r_scbond_it3.067
r_scbond_other3.067
r_mcbond_it2.25
r_mcbond_other2.247
r_angle_refined_deg1.631
r_angle_other_deg0.569
r_nbd_refined0.242
r_xyhbond_nbd_refined0.201
r_symmetry_nbd_refined0.201
r_symmetry_nbd_other0.195
r_symmetry_xyhbond_nbd_refined0.191
r_nbd_other0.177
r_nbtor_refined0.166
r_metal_ion_refined0.103
r_chiral_restr0.08
r_symmetry_nbtor_other0.075
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1000
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing