1Y1O | pdb_00001y1o

X-ray crystal Structure of Penicillin-binding protein-related factor A from Bacillus stearothermophilus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52941.3 M ammonium sulfate, 1% PEG 3350, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
1.933.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.261α = 90
b = 81.018β = 90
c = 106.279γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152004-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794255APS19-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
12.24097.20.101176.63608135057
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)
2.22.26620.5891.422.2

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD2.234.13503035030203897.660.19880.19880.19730.20990.24820.223random36.593
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]
-0.58-0.661.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.96
r_dihedral_angle_4_deg17.458
r_dihedral_angle_3_deg17.322
r_dihedral_angle_1_deg6.141
r_scangle_it4.018
r_scbond_it2.579
r_mcangle_it1.699
r_angle_refined_deg1.459
r_mcbond_it1.13
r_symmetry_hbond_refined0.359
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5512
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing