3D8M

Crystal structure of a chimeric receptor binding protein from lactococcal phages subspecies TP901-1 and p2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BSD	PDB ENTRY 2BSD, 2F0C
experimental model	PDB	2F0C	PDB ENTRY 2BSD, 2F0C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.1M Sodium Cacodylate, 12% MPEG2000, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.833	α = 90
b = 85.833	β = 90
c = 85.833	γ = 90

Symmetry
Space Group	P 21 3

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 210	toroidal mirror	2007-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9340	ESRF	ID14-1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.35	85.75	100	0.245	0.245	15.9	19.9	3206	3206			20.5

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)
1	3.35	3.53	100		0.509	0.509	6.6	20.5	450

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	PDB ENTRY 2BSD, 2F0C	3.35	60.69	2744	2744	450	99.97	0.22853	0.22853	0.22108	0.27437	RANDOM	27.928

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.17
r_dihedral_angle_4_deg	22.051
r_dihedral_angle_3_deg	19.889
r_dihedral_angle_1_deg	5.469
r_scangle_it	1.914
r_angle_refined_deg	1.307
r_scbond_it	1.177
r_mcangle_it	0.784
r_mcbond_it	0.624
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.17
r_dihedral_angle_4_deg	22.051
r_dihedral_angle_3_deg	19.889
r_dihedral_angle_1_deg	5.469
r_scangle_it	1.914
r_angle_refined_deg	1.307
r_scbond_it	1.177
r_mcangle_it	0.784
r_mcbond_it	0.624
r_nbtor_refined	0.312
r_nbd_refined	0.268
r_symmetry_vdw_refined	0.255
r_xyhbond_nbd_refined	0.192
r_symmetry_hbond_refined	0.178
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1137
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
BALBES	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.