Experiment: 6BBD

Structure of N-glycosylated porcine surfactant protein-D complexed with glycerol

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DN8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	Crystallized in hanging drops by mixing 5 ul protein with 5 ul reservoir solution (0.1 M 2-[bis(2-hydroxyethyl)-amino]-2-(hydroxymethyl)propane-1,3-diol, pH 6.5, 0.2 M MgCl2, 15% glycerol, and 22%-20% PEG 3350)

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.798	α = 90
b = 66.798	β = 90
c = 64.974	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	IMAGE PLATE	RIGAKU RAXIS IV++		2012-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	1.9	15	94	0.058	23.2	4.7		12304			35

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	1.9	1.97	67.4		0.356		2.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	4DN8	1.898	14.852	11609	1159	88.75	0.2053	0.2008	0.194	0.2468	0.24	47.29

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]
8.2546			8.2546		-16.5092

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	25.093
f_angle_d	1.085
f_chiral_restr	0.069
f_bond_d	0.014
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1185
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	72

Software

Software
Software Name	Purpose
PHENIX	refinement
DENZO	data collection
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
PHENIX	phasing