3V8L

Crystal structure of Staphylococcus aureus biotin protein ligase in complex with biotinyl-5'-AMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527710% PEG 8000, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.8167.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.665α = 90
b = 93.665β = 90
c = 131.947γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX11.518Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.639.55

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.629.592528813591000.177160.174170.23478RANDOM49.98
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]
-0.12-0.120.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.804
r_dihedral_angle_4_deg24.573
r_dihedral_angle_3_deg16.222
r_dihedral_angle_1_deg6.987
r_scangle_it3.259
r_mcangle_it2.732
r_scbond_it2.144
r_angle_refined_deg1.826
r_mcbond_it1.758
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.804
r_dihedral_angle_4_deg24.573
r_dihedral_angle_3_deg16.222
r_dihedral_angle_1_deg6.987
r_scangle_it3.259
r_mcangle_it2.732
r_scbond_it2.144
r_angle_refined_deg1.826
r_mcbond_it1.758
r_nbtor_refined0.301
r_nbd_refined0.2
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.172
r_symmetry_vdw_refined0.16
r_chiral_restr0.118
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2611
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement