4U3T

Crystal structure of the transpeptidase domain of Neisseria gonorrhoeae penicillin-binding protein 2 derived from the penicillin-resistant strain 6140


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829121% PEG 6000, 0.1 M HEPES pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.1643

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.5α = 90
b = 77.4β = 92.5
c = 88γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

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
12.25096.90.07731.55.3295972959733
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)
12.22.24780.2834.24.1

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3EQU2.235.4529577149696.90.195350.192740.24319RANDOM42.1
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]
3.36-1.21-2.25-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.333
r_dihedral_angle_4_deg19.654
r_dihedral_angle_3_deg16.15
r_dihedral_angle_1_deg6.788
r_angle_refined_deg1.445
r_chiral_restr0.096
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.333
r_dihedral_angle_4_deg19.654
r_dihedral_angle_3_deg16.15
r_dihedral_angle_1_deg6.788
r_angle_refined_deg1.445
r_chiral_restr0.096
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4818
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement