5ZG6

Crystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "post-acylation" 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 3350, 0.4M ammonium acetate
Crystal Properties
Matthews coefficientSolvent content
1.9938.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.292α = 77.43
b = 46.459β = 75.53
c = 65.981γ = 69.34
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2016-08-09MSINGLE 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)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
1263.2940.1130.1350.07383.329472
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)
122.0383.90.3130.3810.2130.8642.8

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 REPLACEMENTTHROUGHOUT4BLM243.0627895148694.270.210750.208190.25845RANDOM16.879
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.334
r_dihedral_angle_4_deg18.882
r_dihedral_angle_3_deg16.268
r_dihedral_angle_1_deg7.554
r_long_range_B_refined4.389
r_long_range_B_other4.385
r_scangle_other2.75
r_angle_other_deg2.393
r_mcangle_it2.163
r_mcangle_other2.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.334
r_dihedral_angle_4_deg18.882
r_dihedral_angle_3_deg16.268
r_dihedral_angle_1_deg7.554
r_long_range_B_refined4.389
r_long_range_B_other4.385
r_scangle_other2.75
r_angle_other_deg2.393
r_mcangle_it2.163
r_mcangle_other2.163
r_scbond_it1.674
r_scbond_other1.674
r_angle_refined_deg1.552
r_mcbond_it1.346
r_mcbond_other1.346
r_chiral_restr0.076
r_bond_other_d0.035
r_gen_planes_other0.011
r_gen_planes_refined0.01
r_bond_refined_d0.008
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 Atoms4012
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing