8OM8

X-ray structure of lysozyme obtained upon reaction with [VIVO(empp)2] (Structure A)


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 pH 4.0
Crystal Properties
Matthews coefficientSolvent content
1.9737.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.06α = 90
b = 78.06β = 90
c = 37.01γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.0ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.0855.4100133.22050384
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)
11.081.10.744

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-VALUE1.0855.25845671231492.1940.150.14760.189520.124
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]
1.6841.684-3.369
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.163
r_dihedral_angle_4_deg17.774
r_rigid_bond_restr14.495
r_dihedral_angle_3_deg12.752
r_dihedral_angle_1_deg6.421
r_scangle_it5.64
r_scangle_other5.606
r_scbond_other5.374
r_scbond_it5.359
r_lrange_it4.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.163
r_dihedral_angle_4_deg17.774
r_rigid_bond_restr14.495
r_dihedral_angle_3_deg12.752
r_dihedral_angle_1_deg6.421
r_scangle_it5.64
r_scangle_other5.606
r_scbond_other5.374
r_scbond_it5.359
r_lrange_it4.65
r_lrange_other4.27
r_angle_refined_deg2.967
r_mcangle_other2.436
r_mcangle_it2.422
r_mcbond_it2.361
r_mcbond_other2.322
r_angle_other_deg1.71
r_nbd_refined0.343
r_symmetry_nbd_other0.257
r_nbd_other0.257
r_xyhbond_nbd_refined0.225
r_symmetry_nbd_refined0.204
r_symmetry_xyhbond_nbd_other0.201
r_nbtor_refined0.193
r_symmetry_xyhbond_nbd_refined0.167
r_chiral_restr0.141
r_symmetry_nbtor_other0.089
r_metal_ion_refined0.042
r_bond_refined_d0.022
r_gen_planes_refined0.014
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing