3G8K | pdb_00003g8k

Crystal structure of murine natural killer cell receptor, Ly49L4

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QO3	PDB ENTRY 1QO3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	25% PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.34	α = 90
b = 90.11	β = 90
c = 90.11	γ = 90

Symmetry
Space Group	I 2 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	IMAGE PLATE	RIGAKU RAXIS IV++	mirrors	2006-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	28.5	98.7	0.081	9.3		22778	22491		2

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)
	2	2.07	95.4		0.407	3.1		2214

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QO3	2	30	21195	1135	98.26	0.22574	0.22108	0.2355	0.288	0.2542	RANDOM	31.061

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]
2.53			-1.35		-1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.262
r_dihedral_angle_4_deg	26.416
r_dihedral_angle_3_deg	19.958
r_dihedral_angle_1_deg	8.345
r_scangle_it	4.829
r_scbond_it	3.487
r_mcangle_it	2.309
r_angle_refined_deg	2.271
r_mcbond_it	1.44
r_nbtor_refined	0.311
r_symmetry_hbond_refined	0.307
r_symmetry_vdw_refined	0.262
r_nbd_refined	0.242
r_xyhbond_nbd_refined	0.2
r_chiral_restr	0.181
r_bond_refined_d	0.025
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2088
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
CrystalClear	data scaling