2ZC5

Penicillin-binding protein 1A (PBP 1A) acyl-enzyme complex (biapenem) from Streptococcus pneumoniae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZC6PDB ENTRY 2ZC6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82930.004-0.006M zinc sulfate, 0.05M MES, pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8256.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 185.704α = 90
b = 50.665β = 90
c = 110.784γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Rotated-inclined double-crystal monochromator, rhodium-coated horizontal mirror2007-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

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
1329.9588.10.136.23.91912750.76
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)
33.1191.50.352.83.6

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 2ZC6329.951813997788.130.22440.221580.276RANDOM50.53
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]
-3.740.972.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.738
r_dihedral_angle_4_deg19.016
r_dihedral_angle_3_deg16.506
r_dihedral_angle_1_deg5.407
r_angle_refined_deg1.01
r_scangle_it0.839
r_mcangle_it0.553
r_scbond_it0.461
r_mcbond_it0.305
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.738
r_dihedral_angle_4_deg19.016
r_dihedral_angle_3_deg16.506
r_dihedral_angle_1_deg5.407
r_angle_refined_deg1.01
r_scangle_it0.839
r_mcangle_it0.553
r_scbond_it0.461
r_mcbond_it0.305
r_nbtor_refined0.303
r_symmetry_vdw_refined0.234
r_nbd_refined0.197
r_symmetry_metal_ion_refined0.156
r_xyhbond_nbd_refined0.135
r_symmetry_hbond_refined0.125
r_metal_ion_refined0.114
r_chiral_restr0.074
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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 Atoms6300
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
BSSdata collection
CrystalCleardata reduction
CrystalCleardata scaling