9QW4 | pdb_00009qw4

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

X-RAY DIFFRACTION

---

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
2.87	57.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.13	α = 90
b = 106.25	β = 91.13
c = 55.34	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	1.85	53.13	98.8	0.061	0.99	9.2	2.5		53663

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	1.85	1.89	98.9		0.333	0.674	3

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	1.85	49.122	53633	2770	98.746	0.18	0.1784	0.1876	0.2008	0.2053	24.891

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]
0.023		-0.16	1.083		-1.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.377
r_dihedral_angle_4_deg	17.236
r_dihedral_angle_3_deg	14.72
r_lrange_it	7.054
r_lrange_other	6.992
r_dihedral_angle_1_deg	5.822
r_scangle_it	5.738
r_scangle_other	5.737
r_scbond_it	3.613
r_scbond_other	3.613
r_mcangle_other	3.193
r_mcangle_it	3.191
r_mcbond_it	2.235
r_mcbond_other	2.23
r_angle_refined_deg	1.64
r_angle_other_deg	1.43
r_nbd_other	0.227
r_nbd_refined	0.224
r_symmetry_nbd_refined	0.2
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.135
r_metal_ion_refined	0.107
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_symmetry_metal_ion_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3441
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	69

Software

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