5EE8

Crystal structure of S02030 boronic acid inhibitor complexed to SHV-1 beta-lactamase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H5S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320-30% PEG 6000, 100mM Tris pH 7.5, 0.56mM cymal-6
Crystal Properties
Matthews coefficientSolvent content
1.9837.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.567α = 90
b = 55.185β = 90
c = 83.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.1271SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.5450970.070.0810.03910.73.633737
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.698.30.420.4920.2460.8123.53365

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2H5S1.5433.332017168696.960.15060.14930.1753RANDOM15.141
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
r_dihedral_angle_2_deg35.509
r_dihedral_angle_4_deg20.409
r_dihedral_angle_3_deg13.004
r_dihedral_angle_1_deg6.144
r_angle_refined_deg1.709
r_mcangle_it1.569
r_mcbond_it1.021
r_mcbond_other1.021
r_angle_other_deg0.94
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.509
r_dihedral_angle_4_deg20.409
r_dihedral_angle_3_deg13.004
r_dihedral_angle_1_deg6.144
r_angle_refined_deg1.709
r_mcangle_it1.569
r_mcbond_it1.021
r_mcbond_other1.021
r_angle_other_deg0.94
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2024
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms97

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing