5E31

2.3 Angstrom Crystal Structure of the Monomeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DVY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7295Protein: 13.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 5mM Penicillin V; Screen: Classics II (H7), 0.15M DL-Malic acid (pH 7.0), 20% (w/v) PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.4750.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.44α = 90
b = 64.34β = 90
c = 182.786γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.329.1299.80.1310.13122.4733135-338.2
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)
12.32.341000.6373.37.2

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 REPLACEMENTTHROUGHOUT5DVY2.329.1230970167798.770.199250.196760.24445RANDOM45.23
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]
-1.47-3.715.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.115
r_dihedral_angle_3_deg10.362
r_dihedral_angle_4_deg8.619
r_long_range_B_refined7.351
r_long_range_B_other7.34
r_scangle_other4.822
r_mcangle_it4.153
r_mcangle_other4.153
r_scbond_it3.013
r_scbond_other3.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.115
r_dihedral_angle_3_deg10.362
r_dihedral_angle_4_deg8.619
r_long_range_B_refined7.351
r_long_range_B_other7.34
r_scangle_other4.822
r_mcangle_it4.153
r_mcangle_other4.153
r_scbond_it3.013
r_scbond_other3.012
r_dihedral_angle_1_deg2.825
r_mcbond_other2.617
r_mcbond_it2.616
r_angle_refined_deg1.517
r_angle_other_deg0.751
r_chiral_restr0.09
r_gen_planes_refined0.022
r_gen_planes_other0.019
r_bond_refined_d0.011
r_bond_other_d0.001
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 Atoms4898
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing