9QW3 | pdb_00009qw3

Crystal structure of human lung surfactant protein D trimeric fragment with bound synthetic HepIII-HepII-HepI ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PWB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	16% PEG 4000 and 0.1 M Tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.24	α = 90
b = 107.56	β = 90.84
c = 55.56	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	PIXEL	DECTRIS PILATUS3 6M		2018-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.63	55.55	98.8	0.051	0.978	9.9	2.6		79745

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.66	98.2		0.345	0.752	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.63	55.295	79704	4242	98.758	0.178	0.1765	0.185	0.1991	0.208	21.667

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]
0.024		-0.023	-0.03		0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.301
r_dihedral_angle_3_deg	13.335
r_dihedral_angle_4_deg	11.854
r_dihedral_angle_1_deg	5.878
r_lrange_it	5.876
r_lrange_other	5.736
r_scangle_it	4.726
r_scangle_other	4.725
r_scbond_it	3.068
r_scbond_other	3.067
r_mcangle_other	2.79
r_mcangle_it	2.789
r_mcbond_it	1.907
r_mcbond_other	1.903
r_angle_refined_deg	1.661
r_angle_other_deg	1.47
r_nbd_refined	0.226
r_nbd_other	0.201
r_symmetry_xyhbond_nbd_refined	0.183
r_symmetry_nbd_other	0.182
r_symmetry_nbd_refined	0.179
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.127
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.08
r_metal_ion_refined	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3374
Nucleic Acid Atoms
Solvent Atoms	371
Heterogen Atoms	78

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
REFMAC	phasing
REFMAC	refinement