2XR0

Room temperature X-ray structure of the perdeuterated Toho-1 R274N R276N double mutant beta-lactamase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WYXPDB ENTRY 2WYX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52.0 A AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PD 5.1. PREPARED IN 99.9% D2O AND MIXED 1:1 WITH PERDEUTERATED PROTEIN PREPARED IN 20 MM NA MES AT PD 6.1 (PH 6.5).
Crystal Properties
Matthews coefficientSolvent content
2.7755.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.5α = 90
b = 73.5β = 90
c = 99.33γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMARRESEARCH MX-3002010-04-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.229.5498.60.0531.37.515962216.86
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)
12.22.3297.90.83227.5

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 2WYX2.229.541.431595680098.20.1350.1330.17319.65
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]
-1.0524-1.05242.1047
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.134
f_angle_d1.122
f_chiral_restr0.07
f_bond_d0.009
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1964
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms15

Software

Software
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing