2ZC3

Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biapenem) from Streptococcus pneumoniae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z2LPDB ENTRY 2Z2L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29310-25% PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7455.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.789α = 90
b = 171.909β = 90
c = 88.666γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VA fixed exit SI double crystal monochromator followed bystandard double crystal monochromator and RH-coated downward-deflection mirror with a typical glancing angle of 3.7MRAD2006-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32B21.0000SPring-8BL32B2

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
12.529.5192.70.05918.95.35371452.76
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)
2.52.5890.10.2285.54.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2Z2L2.529.5150660269193.260.23690.234520.28126RANDOM47.99
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]
2.86-3.530.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.593
r_dihedral_angle_3_deg14.657
r_dihedral_angle_4_deg14.089
r_dihedral_angle_1_deg5.257
r_scangle_it1.037
r_angle_refined_deg0.96
r_mcangle_it0.662
r_scbond_it0.602
r_mcbond_it0.37
r_nbtor_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.593
r_dihedral_angle_3_deg14.657
r_dihedral_angle_4_deg14.089
r_dihedral_angle_1_deg5.257
r_scangle_it1.037
r_angle_refined_deg0.96
r_mcangle_it0.662
r_scbond_it0.602
r_mcbond_it0.37
r_nbtor_refined0.293
r_nbd_refined0.18
r_symmetry_vdw_refined0.131
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.083
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9881
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
BSSdata collection
CrystalCleardata reduction
CrystalCleardata scaling