5ZFT

Crystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "pre-deacylation" intermediate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BLM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2890.1M Tris pH8.0, 25% PEG 33500, 4M ammonium acetate
Crystal Properties
Matthews coefficientSolvent content
1.9737.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.24α = 77.63
b = 45.88β = 75.51
c = 66.09γ = 69.27
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2013-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.9342.4992.80.0510.0590.030.99818.33.932004
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)
11.932.0387.70.1340.1560.0790.9818.43.9

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 REPLACEMENTTHROUGHOUT4BLM1.9335.130373162492.780.179520.177510.21759RANDOM13.767
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.84
r_dihedral_angle_4_deg17.394
r_dihedral_angle_3_deg15.026
r_dihedral_angle_1_deg6.984
r_long_range_B_refined4.632
r_long_range_B_other4.63
r_scangle_other3.101
r_angle_other_deg2.352
r_scbond_it1.896
r_scbond_other1.896
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.84
r_dihedral_angle_4_deg17.394
r_dihedral_angle_3_deg15.026
r_dihedral_angle_1_deg6.984
r_long_range_B_refined4.632
r_long_range_B_other4.63
r_scangle_other3.101
r_angle_other_deg2.352
r_scbond_it1.896
r_scbond_other1.896
r_mcangle_it1.854
r_mcangle_other1.854
r_angle_refined_deg1.834
r_mcbond_it1.162
r_mcbond_other1.153
r_chiral_restr0.089
r_bond_other_d0.034
r_bond_refined_d0.011
r_gen_planes_other0.01
r_gen_planes_refined0.008
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 Atoms4036
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing