1NJ4

Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 1.9 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HD8PDB ENTRY 1HD8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729320% PEG 4000, 100 mM Tris pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4850.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.2α = 90
b = 50.2β = 90
c = 135.76γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2002-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.936.698.70.0737.162977225.9
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)
1.91.9788.40.3541.83.43024

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRefinement from a lower resolution structureTHROUGHOUTPDB ENTRY 1HD81.9152970529705150798.70.20910.209130.207270.24454RANDOM29.263
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]
-0.34-0.17-0.340.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.483
r_dihedral_angle_1_deg3.332
r_scangle_it2.757
r_scbond_it1.633
r_angle_refined_deg1.212
r_mcangle_it1.187
r_mcbond_it0.62
r_nbd_refined0.224
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.169
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.483
r_dihedral_angle_1_deg3.332
r_scangle_it2.757
r_scbond_it1.633
r_angle_refined_deg1.212
r_mcangle_it1.187
r_mcbond_it0.62
r_nbd_refined0.224
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.169
r_symmetry_hbond_refined0.107
r_chiral_restr0.085
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2649
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling