7RPG

X-ray crystal structure of OXA-24/40 K84D in complex with cefotaxime


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PAE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1 M HEPES, 2% v/v PEG 4000, 2.0 M ammonium sulfate

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.447α = 90
b = 102.447β = 90
c = 86.352γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252012-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9787APS21-ID-F

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
11.625098.60.0978.47.758160
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)
11.621.6897.20.766.1

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 REPLACEMENTTHROUGHOUT3PAE1.6227.7654994292898.440.17950.17850.1994RANDOM27.339
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]
-1.44-1.442.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.728
r_dihedral_angle_4_deg20.058
r_dihedral_angle_3_deg14.719
r_dihedral_angle_1_deg5.855
r_angle_refined_deg2.005
r_angle_other_deg1.548
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.728
r_dihedral_angle_4_deg20.058
r_dihedral_angle_3_deg14.719
r_dihedral_angle_1_deg5.855
r_angle_refined_deg2.005
r_angle_other_deg1.548
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1928
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms50

Software

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