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)
Type	Source	Accession Code	Details
experimental model	PDB	2RKZ	PDB ENTRY 2RKZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	CRYSTALS 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 coefficient	Solvent content
2.45	49.7

Crystal Data

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

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD	BENT CYLINDRICAL MIRRORS	2008-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.7	28.22	100	0.05	22.4	6.1		25333		1.9	22.64

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	100		0.41	3.6	6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2RKZ	1.7	26.45	24001	1289	99.98	0.17621	0.17389	0.22157	RANDOM	23.575

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			-0.38		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.26
r_dihedral_angle_4_deg	14.966
r_dihedral_angle_3_deg	10.656
r_dihedral_angle_1_deg	5.862
r_scangle_it	3.7
r_scbond_it	2.334
r_mcangle_it	1.535
r_angle_refined_deg	1.353
r_mcbond_it	0.871
r_nbtor_refined	0.304
r_symmetry_hbond_refined	0.191
r_nbd_refined	0.177
r_symmetry_vdw_refined	0.173
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
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 Atoms	Number
Protein Atoms	1628
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing