5HDH | pdb_00005hdh

Crystal structure of human TLR8 with an uncleaved Z-loop

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	ammonium sulfate, sodium acetate, glycerol

Crystal Properties
Matthews coefficient	Solvent content
4.67	73.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.52	α = 90
b = 171.52	β = 90
c = 301.333	γ = 120

Symmetry
Space Group	H 3 2

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 270		2013-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0000	Photon Factory	AR-NE3A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.6	45.02	100	17.3	19.5		49967

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.6	45.02	49947	2610	99.96	0.20756	0.20589	0.2123	0.23944	0.2429	RANDOM	80.137

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.044
r_long_range_B_other	16.051
r_long_range_B_refined	16.047
r_scangle_other	12.428
r_dihedral_angle_3_deg	10.858
r_mcangle_it	10.53
r_mcangle_other	10.529
r_dihedral_angle_4_deg	9.719
r_scbond_it	8.46
r_scbond_other	8.458
r_mcbond_it	7.607
r_mcbond_other	7.602
r_dihedral_angle_1_deg	1.957
r_angle_refined_deg	1.77
r_angle_other_deg	0.832
r_chiral_restr	0.123
r_gen_planes_refined	0.013
r_bond_refined_d	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	6042
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	250

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data processing
Aimless	data scaling
MOLREP	phasing