2BOX

EGF Domains 1,2,5 of human EMR2, a 7-TM immune system molecule, in complex with strontium.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BOU	PDB ENTRY 2BOU (BARIUM COMPLEX OF THE SAME PROTEIN)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.1 M STRONTIUM CHLORIDE, 12-16% W/V PEG 8000, 0.1 M NA CACODYLATE BUFFER PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.106	α = 90
b = 61.575	β = 90
c = 35.495	γ = 90

Symmetry
Space Group	P 21 21 2

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		2002-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.4	23.26	99.5	0.11	4.8	4.4		8270			0.083

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	2.4	2.53	97.6		0.11	2.1	3.8

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 2BOU (BARIUM COMPLEX OF THE SAME PROTEIN)	2.5	23.262	7342	7342	373		0.2426	0.2426	0.2403	0.2844	RANDOM

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
t_dihedral_angle_d	17.765
t_it	0.778
t_angle_deg	0.641
t_nbd	0.035
t_gen_planes	0.012
t_trig_c_planes	0.005
t_bond_d	0.003
t_incorr_chiral_ct
t_pseud_angle
t_omega_torsion

RMS Deviations
Key	Refinement Restraint Deviation
t_dihedral_angle_d	17.765
t_it	0.778
t_angle_deg	0.641
t_nbd	0.035
t_gen_planes	0.012
t_trig_c_planes	0.005
t_bond_d	0.003
t_incorr_chiral_ct
t_pseud_angle
t_omega_torsion
t_other_torsion
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1014
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	8

Software

Software
Software Name	Purpose
TNT	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	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 R01GM157729.