8AJ5

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429320% ethylene glycol 0.1 M sodium acetate pH 4.0 0.6 M sodium nitrate
Crystal Properties
Matthews coefficientSolvent content
1.9938.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.23α = 90
b = 78.23β = 90
c = 37.28γ = 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
11.3155.3298.90.1410.99714.32028122
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)
11.311.3398.91.80.75525.8

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-VALUE193l1.3155.31728065140398.7790.1690.16760.197618.925
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]
0.0370.037-0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.266
r_dihedral_angle_4_deg20.745
r_dihedral_angle_3_deg13.831
r_lrange_it6.649
r_lrange_other6.648
r_dihedral_angle_1_deg6.465
r_scangle_it4.264
r_scangle_other4.131
r_scbond_it2.905
r_scbond_other2.787
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.266
r_dihedral_angle_4_deg20.745
r_dihedral_angle_3_deg13.831
r_lrange_it6.649
r_lrange_other6.648
r_dihedral_angle_1_deg6.465
r_scangle_it4.264
r_scangle_other4.131
r_scbond_it2.905
r_scbond_other2.787
r_mcangle_other2.39
r_mcangle_it2.389
r_angle_refined_deg1.839
r_mcbond_it1.67
r_mcbond_other1.616
r_angle_other_deg1.58
r_nbd_refined0.276
r_nbd_other0.27
r_xyhbond_nbd_refined0.236
r_symmetry_nbd_refined0.216
r_symmetry_xyhbond_nbd_refined0.211
r_symmetry_nbd_other0.2
r_nbtor_refined0.174
r_symmetry_metal_ion_refined0.119
r_metal_ion_refined0.099
r_chiral_restr0.093
r_symmetry_nbtor_other0.089
r_symmetry_xyhbond_nbd_other0.084
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 Atoms132
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing