3CZF | pdb_00003czf

Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide (residues 412-420)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K5N	PDB ENTRY 1K5N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	291	14% (w/v) PEG 4000, 20mM Tris/HCl pH 7.5, 150mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.946	α = 90
b = 81.933	β = 108.91
c = 65.397	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	100	CCD	ADSC QUANTUM 4		2003-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.1	30	95.8	0.043	20.8			196702		-3	14.7

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	1.1	1.12	90.4		0.288	2.7

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 1K5N	1.2	15	149186	3852	96.8	0.13	0.129	0.14	0.149	0.16	RANDOM	10.87

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]
0.12		-0.22	-0.15		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.892
r_dihedral_angle_4_deg	15.724
r_dihedral_angle_3_deg	11.31
r_sphericity_free	6.433
r_dihedral_angle_1_deg	6.098
r_sphericity_bonded	3.849
r_scangle_it	3.398
r_scbond_it	2.645
r_mcangle_it	1.983
r_mcbond_it	1.696
r_rigid_bond_restr	1.453
r_angle_refined_deg	1.427
r_angle_other_deg	0.905
r_mcbond_other	0.631
r_symmetry_vdw_other	0.311
r_nbd_refined	0.214
r_nbd_other	0.209
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.145
r_symmetry_hbond_refined	0.143
r_symmetry_vdw_refined	0.096
r_chiral_restr	0.094
r_nbtor_other	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3192
Nucleic Acid Atoms
Solvent Atoms	711
Heterogen Atoms	18

Software

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