1HD8

Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1720% POLYETHYLENE GLYCOL 4000, 50 MM TRIS PH 7.0, 0.2 % SODIUM AZIDE
Crystal Properties
Matthews coefficientSolvent content
3.0659.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.83α = 90
b = 50.83β = 90
c = 140.29γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMACSCIENCEMIRRORS1998-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODENONIUS FR391

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.322.494.80.06913.22.521723928.41
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3885.20.2943.31.9

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 DIFFRACTIONMIRTHROUGHOUT2.31517184169395.40.2070.1990.283RANDOM35.44
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor22.8
p_staggered_tor19.9
p_planar_tor9.8
p_scangle_it2.92
p_mcangle_it2.541
p_scbond_it1.864
p_mcbond_it1.642
p_multtor_nbd0.257
p_singtor_nbd0.191
p_xyhbond_nbd0.187
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor22.8
p_staggered_tor19.9
p_planar_tor9.8
p_scangle_it2.92
p_mcangle_it2.541
p_scbond_it1.864
p_mcbond_it1.642
p_multtor_nbd0.257
p_singtor_nbd0.191
p_xyhbond_nbd0.187
p_chiral_restr0.148
p_planar_d0.074
p_angle_d0.043
p_plane_restr0.0244
p_bond_d0.013
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2606
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing