5JFB

Crystal structure of the scavenger receptor cysteine-rich domain 5 (SRCR5) from porcine CD163

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BY2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	25% (w/v) PEG 4000, 200mM (NH4)2SO4 in 100mM sodium acetate at pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.711	α = 90
b = 73.93	β = 90
c = 87.527	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CMOS	Pilatus		2015-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.979	SSRF	BL19U1

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	2	50	97.1	0.107	17.7	10		6682

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1BY2	2	43.76	6223	319	95.31	0.20922	0.20767	0.23905	RANDOM	23.6

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]
-0.36			0.16		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.554
r_dihedral_angle_4_deg	18.415
r_dihedral_angle_3_deg	13.139
r_dihedral_angle_1_deg	7.337
r_long_range_B_refined	4.212
r_long_range_B_other	4.175
r_scangle_other	2.242
r_mcangle_it	1.744
r_mcangle_other	1.743
r_scbond_it	1.391
r_scbond_other	1.383
r_angle_refined_deg	1.276
r_mcbond_other	1.047
r_mcbond_it	1.046
r_angle_other_deg	0.92
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	761
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data processing
HKL-3000	data scaling