8HYD

Crystal structure of B1 VIM-2 MBL in complex with 2-amino-5-(2-(thiophen-2-yl)ethyl)thiazole-4-carboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico model 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2M Magnesium Formate, 28%-35% (v/v) Polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.7354.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.009α = 90
b = 64.533β = 90
c = 90.678γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray195PIXELDECTRIS PILATUS3 X CdTe 1M2021-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U11SSRFBL19U1

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
11.7119.8995.680.99920.712.728787
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)
11.711.770.742

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7DV01.7119.5511.627110200090.220.16850.16590.2013
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.67
f_angle_d1.058
f_chiral_restr0.063
f_bond_d0.016
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1733
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms18

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling