4QKJ | pdb_00004qkj

Glycosylated form of human LLT1, a ligand for NKR-P1, in this structure forming hexamers

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HUP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	288	40%(v/v) PEG300 and 0.1M citrate phosphate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.06	α = 90
b = 70.06	β = 90
c = 101.71	γ = 120

Symmetry
Space Group	P 63 2 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	MARMOSAIC 225 mm CCD	Si Mirror, double crystal Si monochromator, Rh mirror	2011-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	2.7	39	99.5	0.093	16.2	4.3	4431	4431		-3	66.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.76	99.3		0.757	2	4.4	273

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 (except for the last cycle)	3HUP	2.75	39	4186	4186	223	99.52	0.23022	0.23022	0.22133	0.23	0.2978	0.23	RANDOM	40.052

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]
-0.16	-0.08		-0.16		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.451
r_dihedral_angle_3_deg	21.562
r_dihedral_angle_4_deg	14.554
r_long_range_B_refined	10.195
r_long_range_B_other	10.192
r_dihedral_angle_1_deg	9.828
r_mcangle_it	6.515
r_mcangle_other	6.51
r_scangle_other	6.07
r_mcbond_it	3.959
r_mcbond_other	3.957
r_scbond_it	3.78
r_scbond_other	3.777
r_angle_refined_deg	1.967
r_angle_other_deg	0.971
r_chiral_restr	0.108
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.006
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	945
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	14

Software

Software
Software Name	Purpose
MxCuBE	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Sawaya	data scaling