1YCJ | pdb_00001ycj

Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	279	PEG4000, phosphat-citrate buffer, lithiumsulphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.714	α = 90
b = 57.901	β = 102.51
c = 88.75	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARRESEARCH		2004-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8128	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.94	25	99.7	0.05	18.5	3.1	37489	37372	-3	3	26.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.94	2.01	100		0.314	3.9		3721

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-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	1FTJ	1.95	20.3	35600	1875	99.46	0.20295	0.20295	0.19941	0.2	0.26885	0.27	RANDOM	29.497

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]
1.11		-0.95	-0.59		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.676
r_dihedral_angle_3_deg	17.347
r_dihedral_angle_4_deg	16.866
r_dihedral_angle_1_deg	7.116
r_scangle_it	4.314
r_scbond_it	2.955
r_mcangle_it	1.994
r_angle_refined_deg	1.876
r_mcbond_it	1.312
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.255
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.196
r_symmetry_hbond_refined	0.159
r_chiral_restr	0.142
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4038
Nucleic Acid Atoms
Solvent Atoms	398
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing