8AJ3

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 DROP42932.0 M sodium formate and 0.1 M Hepes, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
1.9637.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.89α = 90
b = 76.89β = 90
c = 38.05γ = 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
11.1354.3797.30.060.99928.416.142289
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)
11.131.1587.90.3390.9263.45

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-VALUE193L1.1354.36942156209197.4640.2020.19940.249316.146
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]
-0.855-0.8551.709
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.195
r_dihedral_angle_4_deg18.888
r_dihedral_angle_3_deg13.348
r_dihedral_angle_1_deg6.497
r_rigid_bond_restr6.465
r_lrange_it3.978
r_scangle_it3.532
r_scbond_it3.067
r_mcangle_it2.322
r_mcbond_it2.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.195
r_dihedral_angle_4_deg18.888
r_dihedral_angle_3_deg13.348
r_dihedral_angle_1_deg6.497
r_rigid_bond_restr6.465
r_lrange_it3.978
r_scangle_it3.532
r_scbond_it3.067
r_mcangle_it2.322
r_mcbond_it2.014
r_angle_refined_deg1.883
r_nbtor_refined0.308
r_symmetry_xyhbond_nbd_refined0.279
r_metal_ion_refined0.242
r_nbd_refined0.22
r_xyhbond_nbd_refined0.202
r_symmetry_nbd_refined0.184
r_chiral_restr0.129
r_gen_planes_refined0.013
r_bond_refined_d0.012
r_ext_dist_refined_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing