5LCH

VIM-2 metallo-beta-lactamase in complex with (S)-1-allyl-2-(3-methoxyphenyl)-3-oxoisoindoline-4-carboxylic acid (compound 42)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4C1D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52950.1 M Magnesium Formate, 24.5% (v/v) Polyethylene glycol 3350, 1 mM Tris(2-carboxyethyl)phosphine, 5 mM (S)-1-allyl-2-(3-methoxyphenyl)-3-oxoisoindoline-4-carboxylic acid, 16 mg/mL protein
Crystal Properties
Matthews coefficientSolvent content
2.1242.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.87α = 90
b = 67.84β = 91.75
c = 40.35γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+OSMIC HF2016-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.542

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.9420.1799.40.0530.0640.0350.99714.63.11588410.17
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.941.9999.10.1172.3

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 REPLACEMENTFREE R-VALUE4C1D1.9420.1651.3815867158399.330.12890.12530.161213.5849
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_d11.123
f_angle_d0.816
f_chiral_restr0.053
f_bond_d0.013
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1714
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms26

Software

Software
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
CrystalCleardata reduction
HKL-3000data reduction