2HB9

Crystal Structure of the Zinc-Beta-Lactamase L1 from Stenotrophomonas Maltophilia (Inhibitor 3)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SMLPDB ENTRY 1SML

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.752811.8M AMMONIUM SULFATE, 0.1M HEPES PH 7.75, 1.5% V/V PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.09α = 90
b = 104.09β = 90
c = 98.21γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2006-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5711.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.7519.5199.60.0590.05411.26.731993319932
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8499.60.3810.28725.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1SML1.7519.673199330361162399.430.170810.16970.1912RANDOM16.876
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]
-0.02-0.01-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.232
r_dihedral_angle_4_deg19.45
r_dihedral_angle_3_deg13.107
r_dihedral_angle_1_deg6.281
r_scangle_it2.994
r_scbond_it1.854
r_angle_refined_deg1.581
r_mcangle_it1.158
r_mcbond_it0.705
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.232
r_dihedral_angle_4_deg19.45
r_dihedral_angle_3_deg13.107
r_dihedral_angle_1_deg6.281
r_scangle_it2.994
r_scbond_it1.854
r_angle_refined_deg1.581
r_mcangle_it1.158
r_mcbond_it0.705
r_nbtor_refined0.306
r_nbd_refined0.279
r_symmetry_vdw_refined0.194
r_metal_ion_refined0.134
r_xyhbond_nbd_refined0.117
r_symmetry_hbond_refined0.116
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2001
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms40

Software

Software
Software NamePurpose
XDSdata scaling
SCALAdata scaling
CCP4model building
REFMACrefinement
XDSdata reduction
CCP4phasing