2NYP

Structure of beta-lactamase II from Bacillus cereus. R121H, C221D doble mutant with two zinc ions.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BC2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.42950.1 M sodium cacodylate,60 mM sodium tartrate, 18% PEG 3350, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2645.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.464α = 90
b = 61.023β = 92.92
c = 68.71γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.42LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.845097.60.04712.42.61846145536
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.841.9186.30.2772.92.3

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 REPLACEMENTTHROUGHOUT1bc21.8468.681846194797.870.1820.1790.241RANDOM23.794
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]
-0.890.52-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.195
r_dihedral_angle_4_deg20.016
r_dihedral_angle_3_deg13.09
r_dihedral_angle_1_deg6.415
r_scangle_it3.748
r_scbond_it2.421
r_mcangle_it1.584
r_angle_refined_deg1.566
r_mcbond_it0.986
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.195
r_dihedral_angle_4_deg20.016
r_dihedral_angle_3_deg13.09
r_dihedral_angle_1_deg6.415
r_scangle_it3.748
r_scbond_it2.421
r_mcangle_it1.584
r_angle_refined_deg1.566
r_mcbond_it0.986
r_nbtor_refined0.311
r_symmetry_vdw_refined0.221
r_nbd_refined0.209
r_xyhbond_nbd_refined0.171
r_symmetry_hbond_refined0.166
r_chiral_restr0.108
r_bond_refined_d0.015
r_metal_ion_refined0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1668
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing