2I8C

Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I87PDB ENTRY 2I87

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.1642.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.802α = 90
b = 66.972β = 96.05
c = 78.992γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirror2001-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
12.4679990.070.0723.93.7250172374140
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5999.20.6210.62123.71329

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2I872.4647.512501723741125497.180.212830.209880.26926RANDOM45.406
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]
2.43-1.44-2.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.023
r_dihedral_angle_4_deg21.081
r_dihedral_angle_3_deg19.356
r_dihedral_angle_1_deg7.761
r_scangle_it3
r_scbond_it2.019
r_angle_refined_deg1.776
r_mcangle_it1.262
r_mcbond_it1.049
r_angle_other_deg0.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.023
r_dihedral_angle_4_deg21.081
r_dihedral_angle_3_deg19.356
r_dihedral_angle_1_deg7.761
r_scangle_it3
r_scbond_it2.019
r_angle_refined_deg1.776
r_mcangle_it1.262
r_mcbond_it1.049
r_angle_other_deg0.981
r_symmetry_vdw_other0.255
r_nbd_refined0.232
r_nbd_other0.206
r_nbtor_refined0.193
r_symmetry_hbond_refined0.191
r_symmetry_vdw_refined0.189
r_mcbond_other0.156
r_xyhbond_nbd_refined0.152
r_chiral_restr0.095
r_nbtor_other0.095
r_xyhbond_nbd_other0.091
r_bond_refined_d0.018
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5496
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement