4ZJ1

Crystal Structure of p-acrylamido-phenylalanine modified TEM1 beta-lactamase from Escherichia coli : V216AcrF mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BTLPDB entry 1BTL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82950.1M 2-(N-morpholino) ethanesulfonic acid (MES) pH 6.5, 15% PEG 20.000 and 15% PEG 550MME
Crystal Properties
Matthews coefficientSolvent content
2.0941.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.47α = 90
b = 47.24β = 90
c = 128.33γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2014-09-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.5426.541000.06416.37.441549
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)
11.541.631000.1886.57.1

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 REPLACEMENTTHROUGHOUTPDB entry 1BTL1.542539324208299.760.141850.140350.17045RANDOM16.414
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]
1.26-0.52-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.678
r_dihedral_angle_4_deg14.991
r_dihedral_angle_3_deg11.673
r_long_range_B_refined7.42
r_long_range_B_other7.419
r_dihedral_angle_1_deg5.678
r_scangle_other4.02
r_scbond_it2.675
r_scbond_other2.674
r_mcangle_other2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.678
r_dihedral_angle_4_deg14.991
r_dihedral_angle_3_deg11.673
r_long_range_B_refined7.42
r_long_range_B_other7.419
r_dihedral_angle_1_deg5.678
r_scangle_other4.02
r_scbond_it2.675
r_scbond_other2.674
r_mcangle_other2.09
r_mcangle_it2.084
r_angle_refined_deg1.851
r_mcbond_it1.396
r_mcbond_other1.354
r_angle_other_deg1.04
r_chiral_restr0.252
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2050
Nucleic Acid Atoms
Solvent Atoms468
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing