8PFX

X-ray structure of the adduct formed upon reaction of Lysozyme with K2[Ru2(D-p-FPhF)(CO3)3] in condition B


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52932 M sodium formate and 0.1 M Hepes, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.0138.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.72α = 90
b = 76.72β = 90
c = 38.39γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-06-13MSINGLE 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
11.0338.361000.034133.711.457486
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)
11.031.040.7530.8582.3

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-VALUE1.0338.3655049272196.3910.1930.1920.214412.285
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]
-0.025-0.0250.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.482
r_dihedral_angle_3_deg12.733
r_dihedral_angle_2_deg10.403
r_dihedral_angle_1_deg5.993
r_lrange_it5.31
r_lrange_other4.991
r_scangle_other3.714
r_scangle_it3.638
r_scbond_it2.397
r_scbond_other2.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.482
r_dihedral_angle_3_deg12.733
r_dihedral_angle_2_deg10.403
r_dihedral_angle_1_deg5.993
r_lrange_it5.31
r_lrange_other4.991
r_scangle_other3.714
r_scangle_it3.638
r_scbond_it2.397
r_scbond_other2.317
r_angle_refined_deg1.933
r_mcangle_other1.742
r_mcangle_it1.735
r_mcbond_it1.202
r_mcbond_other1.201
r_angle_other_deg0.635
r_symmetry_xyhbond_nbd_refined0.295
r_nbd_refined0.249
r_nbd_other0.206
r_symmetry_nbd_other0.204
r_xyhbond_nbd_refined0.198
r_nbtor_refined0.186
r_symmetry_nbd_refined0.185
r_chiral_restr0.102
r_symmetry_nbtor_other0.081
r_xyhbond_nbd_other0.079
r_metal_ion_refined0.061
r_symmetry_xyhbond_nbd_other0.03
r_bond_refined_d0.013
r_gen_planes_refined0.01
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 Atoms137
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing