2ORK | pdb_00002ork

crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with inositol-1-phosphate

X-RAY DIFFRACTION

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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
3.21	61.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.403	α = 90
b = 108.01	β = 91.83
c = 55.701	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		2006-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	1.0	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	1.9	38.66	92.7	0.038	0.038	46.2	3.8	51917	48123

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)
	1.9	1.97	72.6		0.067	0.067	17	2	3737

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 (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 2GGU	1.89	38.66	47776	44155	3900	92.42	0.18964	0.18964	0.18642	0.22611	0.2696	RANDOM	21.249

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]
0.07		0.32	0.15		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.579
r_dihedral_angle_4_deg	13.889
r_dihedral_angle_3_deg	12.862
r_dihedral_angle_1_deg	5.477
r_scangle_it	3.659
r_scbond_it	2.284
r_mcangle_it	1.385
r_angle_refined_deg	1.247
r_mcbond_it	1.082
r_nbtor_refined	0.3
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.199
r_symmetry_hbond_refined	0.165
r_metal_ion_refined	0.164
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3457
Nucleic Acid Atoms
Solvent Atoms	517
Heterogen Atoms	41

Software

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