5U2G

2.6 Angstrom Resolution Crystal Structure of Penicillin-Binding Protein 1A from Haemophilus influenzae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5295Protein: 9.3 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen: Classics II (G5), 0.2M Lithium sulfate, 0.1M Tris (pH 8.5), 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.856.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.448α = 90
b = 111.928β = 90.4
c = 107.693γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2016-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
12.63099.80.0830.08323.43.862896-369.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6499.70.6840.7922.13.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.6129.1559853300398.920.180740.178570.22277RANDOM76.578
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]
0.49-0.224.76-5.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.227
r_dihedral_angle_4_deg10.21
r_dihedral_angle_3_deg9.657
r_long_range_B_refined6.651
r_long_range_B_other6.573
r_scangle_other4.43
r_mcangle_it3.942
r_mcangle_other3.942
r_scbond_it2.814
r_scbond_other2.814
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.227
r_dihedral_angle_4_deg10.21
r_dihedral_angle_3_deg9.657
r_long_range_B_refined6.651
r_long_range_B_other6.573
r_scangle_other4.43
r_mcangle_it3.942
r_mcangle_other3.942
r_scbond_it2.814
r_scbond_other2.814
r_dihedral_angle_1_deg2.48
r_mcbond_it2.458
r_mcbond_other2.458
r_angle_refined_deg1.376
r_angle_other_deg0.9
r_chiral_restr0.087
r_gen_planes_refined0.023
r_gen_planes_other0.019
r_bond_refined_d0.008
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 Atoms10449
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing