7MSG | pdb_00007msg

The crystal structure of LIGHT in complex with HVEM and CD160

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RSU	4RSU, 6NG9
experimental model	PDB	6NG9	4RSU, 6NG9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	291	0.2 M potassium iodide, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 214.689	α = 90
b = 214.689	β = 90
c = 214.689	γ = 90

Symmetry
Space Group	I 2 3

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	MARMOSAIC 225 mm CCD		2016-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	3.5	34.83	99.9	0.195	0.2	0.044	0.999	16.1	20.7		20868

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.5	3.83	100		1.718	1.767	0.414	0.676		17.9

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	THROUGHOUT	4RSU, 6NG9	3.5	19.933	20765	1001	99.33	0.258	0.2566	0.25	0.2847	0.28	139.931

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.315
r_dihedral_angle_3_deg	16.113
r_dihedral_angle_4_deg	14.992
r_lrange_other	13.762
r_lrange_it	13.761
r_dihedral_angle_1_deg	7.187
r_mcangle_it	7.14
r_mcangle_other	7.14
r_scangle_it	5.843
r_scangle_other	5.843
r_mcbond_it	4.082
r_mcbond_other	4.079
r_scbond_it	3.215
r_scbond_other	3.214
r_angle_other_deg	1.52
r_angle_refined_deg	1.29
r_symmetry_nbd_refined	0.386
r_nbd_other	0.349
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.193
r_nbd_refined	0.161
r_nbtor_refined	0.153
r_xyhbond_nbd_refined	0.134
r_symmetry_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.047
r_bond_other_d	0.012
r_gen_planes_other	0.006
r_bond_refined_d	0.005
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7929
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	201

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing