2RKZ

Crystal structure of the second and third fibronectin f1 modules in complex with a fragment of staphylococcus aureus fnbpa-1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		A previous lower resolution structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	0.8M SUCCINIC ACID, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.59	α = 90
b = 109.72	β = 96.94
c = 71.47	γ = 90

Symmetry
Space Group	P 1 21 1

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 QUANTUM 315	Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror	2006-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97620	ESRF	ID29

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	26.038	99.9	0.1	0.1	11.5	3.6	61539	58424		3.7	19.1

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)	Redundancy	Number Unique Reflections (All)
	2	2.11	100		0.272	0.272	4.2	3.7	8970

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	A previous lower resolution structure	2	25.58	61510	58424	3086	99.97	0.2	0.2	0.197	0.261	RANDOM	24.358

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]
3.64		-0.13	-2.17		-1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.418
r_dihedral_angle_1_deg	23.122
r_dihedral_angle_4_deg	18.765
r_dihedral_angle_3_deg	16.566
r_scangle_it	9.292
r_scbond_it	6.619
r_mcangle_it	4.349
r_mcbond_it	3.106
r_angle_refined_deg	1.423
r_symmetry_hbond_refined	0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.418
r_dihedral_angle_1_deg	23.122
r_dihedral_angle_4_deg	18.765
r_dihedral_angle_3_deg	16.566
r_scangle_it	9.292
r_scbond_it	6.619
r_mcangle_it	4.349
r_mcbond_it	3.106
r_angle_refined_deg	1.423
r_symmetry_hbond_refined	0.35
r_nbtor_refined	0.338
r_nbd_refined	0.31
r_symmetry_vdw_refined	0.288
r_xyhbond_nbd_refined	0.228
r_chiral_restr	0.028
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5078
Nucleic Acid Atoms
Solvent Atoms	822
Heterogen Atoms	28

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.