5XGT

Crystal structure of the N-terminal domain of Staphylococcus aureus single-stranded DNA-binding protein SsbA at 1.82 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X3E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529822% PEG 4000, 100mM HEPES sodium salt pH 7.5, 100mM sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.4148.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.792α = 90
b = 88.792β = 90
c = 57.686γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 2102015-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C10.975NSRRCBL13C1

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
11.823099.90.07527.478.623485
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.999.94.28.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT1X3E1.823020126109599.880.195250.193230.23311RANDOM31.221
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]
0.460.46-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.851
r_dihedral_angle_4_deg17.721
r_dihedral_angle_3_deg14.895
r_long_range_B_other8.447
r_long_range_B_refined8.444
r_dihedral_angle_1_deg6.968
r_scangle_other5.883
r_mcangle_it4.787
r_mcangle_other4.785
r_scbond_it3.704
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.851
r_dihedral_angle_4_deg17.721
r_dihedral_angle_3_deg14.895
r_long_range_B_other8.447
r_long_range_B_refined8.444
r_dihedral_angle_1_deg6.968
r_scangle_other5.883
r_mcangle_it4.787
r_mcangle_other4.785
r_scbond_it3.704
r_scbond_other3.702
r_mcbond_other3.021
r_mcbond_it3.02
r_angle_refined_deg1.86
r_angle_other_deg0.867
r_chiral_restr0.112
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1651
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing