2RKY

Crystal structure of the fourth and fifth fibronectin F1 modules in complex with a fragment of staphylococcus aureus fnbpa-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherPrevious lower resolution structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291100mM Tris-HCl, pH8.5, 0.15M Potassium thiocyanate, 20% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2244.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.596α = 90
b = 36.244β = 90
c = 73.551γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

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
11.830.5199.70.0640.064297.121474214743.720.1
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)
1.81.8698.970.4880.4886.37.21630

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 DIFFRACTIONTHROUGHOUTPrevious lower resolution structure1.830.513.72261621474114299.70.1830.1830.1810.216RANDOM22.819
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]
0.03-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.507
r_dihedral_angle_3_deg12.646
r_dihedral_angle_4_deg12.502
r_dihedral_angle_1_deg6.236
r_scangle_it4.524
r_mcangle_it3.673
r_scbond_it3.153
r_mcbond_it2.426
r_angle_refined_deg1.38
r_symmetry_vdw_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.507
r_dihedral_angle_3_deg12.646
r_dihedral_angle_4_deg12.502
r_dihedral_angle_1_deg6.236
r_scangle_it4.524
r_mcangle_it3.673
r_scbond_it3.153
r_mcbond_it2.426
r_angle_refined_deg1.38
r_symmetry_vdw_refined0.311
r_nbtor_refined0.298
r_nbd_refined0.229
r_symmetry_hbond_refined0.184
r_xyhbond_nbd_refined0.141
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_chiral_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1775
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms16

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction