8H7J | pdb_00008h7j

The crystal structure of CD163 SRCR5-9

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	20% PEG 4000, 0.15M potassium sodium tartrate tetra-hydrate pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.328	α = 90
b = 60.085	β = 114.12
c = 85.424	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER X 16M		2018-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.5	50	98.7	0.139	0.059	0.996	21.1	6.4		20350

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	96.6		1.552	0.779	0.761	2.2	4.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5JFB	2.5	48.487	19455	936	94.031	0.184	0.1822	0.19	0.2123	0.21	59.455

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]
-0.066		0.067	-0.411		0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	16.707
r_lrange_it	16.699
r_dihedral_angle_6_deg	15.669
r_scangle_it	15.447
r_scangle_other	15.444
r_dihedral_angle_3_deg	12.889
r_scbond_it	12.502
r_scbond_other	12.499
r_mcangle_it	12.185
r_mcangle_other	12.184
r_mcbond_it	9.908
r_mcbond_other	9.885
r_dihedral_angle_1_deg	7.683
r_dihedral_angle_2_deg	4.186
r_angle_refined_deg	1.437
r_angle_other_deg	0.552
r_symmetry_nbd_refined	0.194
r_symmetry_nbd_other	0.185
r_symmetry_xyhbond_nbd_refined	0.176
r_nbd_other	0.169
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.155
r_nbd_refined	0.146
r_symmetry_nbtor_other	0.1
r_chiral_restr	0.063
r_symmetry_xyhbond_nbd_other	0.041
r_gen_planes_refined	0.019
r_gen_planes_other	0.017
r_bond_refined_d	0.009
r_bond_other_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4130
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	156

Software

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