2OS9

crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with myoinositol

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	150mM NaCl, 10mM CaCl2, 12% PEG 8000, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.564	α = 90
b = 108.692	β = 91.49
c = 55.774	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 4		2005-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	1.1	NSLS	X8C

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	1.7	27.9	94.7	0.04	0.04	23.4	3.2	72901	69027

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)
	1.7	1.76	87.7		0.26	0.26	4	3	6343

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2GGU	1.7	27.87	66682	61994	5502	92.97	0.19724	0.19492	0.22274	RANDOM	26.244

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]
-0.19		-0.37	1.16		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.145
r_dihedral_angle_4_deg	12.702
r_dihedral_angle_3_deg	12.536
r_dihedral_angle_1_deg	5.259
r_scangle_it	3.425
r_scbond_it	2.151
r_mcangle_it	1.366
r_angle_refined_deg	1.216
r_mcbond_it	0.972
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.145
r_dihedral_angle_4_deg	12.702
r_dihedral_angle_3_deg	12.536
r_dihedral_angle_1_deg	5.259
r_scangle_it	3.425
r_scbond_it	2.151
r_mcangle_it	1.366
r_angle_refined_deg	1.216
r_mcbond_it	0.972
r_nbtor_refined	0.302
r_nbd_refined	0.205
r_symmetry_hbond_refined	0.2
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.074
r_metal_ion_refined	0.07
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3454
Nucleic Acid Atoms
Solvent Atoms	515
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	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.