7RPC

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.1 M TRIS HCL, 2.0 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
4.1870.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.828α = 90
b = 102.828β = 90
c = 87.433γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252015-06-15MSINGLE 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)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
12.585096.10.120.1290.0476.27.814713
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)
12.582.671000.6480.6930.2430.9478.1

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 REPLACEMENTTHROUGHOUT3PAE2.5846.031393273796.030.21880.21550.2866RANDOM53.652
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]
-4.93-4.939.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.396
r_dihedral_angle_3_deg18.038
r_dihedral_angle_4_deg16.699
r_dihedral_angle_1_deg6.514
r_angle_refined_deg1.946
r_chiral_restr0.126
r_angle_other_deg0.01
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1893
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms33

Software

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