8AJ4

X-ray structure of lysozyme obtained upon reaction with [VIVO(malt)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 DROP7.52932.0 M sodium formate 0.1 M hepes pH 7.5
Crystal Properties
Matthews coefficientSolvent content
1.9737.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.08α = 90
b = 77.08β = 90
c = 38.09γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-07-28MSINGLE 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
11.2238.5499.70.090.99919.118.634981
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)
11.221.2497.31.0050.7473.112.4

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-VALUE193L1.2238.5434951172899.6950.1790.17770.202617.152
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]
-0.03-0.030.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.437
r_dihedral_angle_4_deg22.202
r_dihedral_angle_3_deg13.275
r_dihedral_angle_1_deg6.17
r_lrange_other5.701
r_lrange_it5.532
r_scangle_other3.789
r_scangle_it3.642
r_scbond_other2.413
r_scbond_it2.344
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.437
r_dihedral_angle_4_deg22.202
r_dihedral_angle_3_deg13.275
r_dihedral_angle_1_deg6.17
r_lrange_other5.701
r_lrange_it5.532
r_scangle_other3.789
r_scangle_it3.642
r_scbond_other2.413
r_scbond_it2.344
r_mcangle_other2.251
r_mcangle_it2.239
r_angle_refined_deg1.813
r_angle_other_deg1.603
r_mcbond_it1.505
r_mcbond_other1.469
r_nbd_refined0.24
r_symmetry_nbd_other0.194
r_nbd_other0.186
r_xyhbond_nbd_refined0.185
r_nbtor_refined0.175
r_symmetry_xyhbond_nbd_refined0.165
r_symmetry_nbd_refined0.148
r_metal_ion_refined0.123
r_chiral_restr0.106
r_symmetry_nbtor_other0.085
r_bond_refined_d0.019
r_gen_planes_refined0.016
r_ext_dist_refined_d0.009
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 Atoms141
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing