3ZRZ

Crystal structure of the second and third fibronectin F1 modules in complex with a fragment of Streptococcus pyogenes SfbI-5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RKZPDB ENTRY 2RKZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7291CRYSTALS OF THE PROTEIN/PEPTIDE COMPLEX (0.3 MM/3.5 MM, PH 7.7) WERE GROWN USING SITTING DROP VAPOUR DIFFUSION FROM A 1:1 DILUTION WITH WELL SOLUTION (0.1 M TRIS PH 7.0, 1.5 M (NH4)2SO4 AT 18 DEGREES CENTIGRADE
Crystal Properties
Matthews coefficientSolvent content
2.4549.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.055α = 90
b = 50.055β = 90
c = 93.504γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDBENT CYLINDRICAL MIRRORS2008-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.728.221000.0522.46.1253331.922.64
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)
11.71.791000.413.66.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2RKZ1.726.4524001128999.980.176210.173890.22157RANDOM23.575
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]
-0.38-0.380.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.26
r_dihedral_angle_4_deg14.966
r_dihedral_angle_3_deg10.656
r_dihedral_angle_1_deg5.862
r_scangle_it3.7
r_scbond_it2.334
r_mcangle_it1.535
r_angle_refined_deg1.353
r_mcbond_it0.871
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.26
r_dihedral_angle_4_deg14.966
r_dihedral_angle_3_deg10.656
r_dihedral_angle_1_deg5.862
r_scangle_it3.7
r_scbond_it2.334
r_mcangle_it1.535
r_angle_refined_deg1.353
r_mcbond_it0.871
r_nbtor_refined0.304
r_symmetry_hbond_refined0.191
r_nbd_refined0.177
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.153
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.007
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1628
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing