1OF2 | pdb_00001of2

Crystal structure of HLA-B*2709 complexed with the vasoactive intestinal peptide type 1 receptor (VIPR) peptide (residues 400-408)

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	VAPOR DIFFUSION, HANGING DROP	8.5	291	TRIS PH 8.5, 19% PEG 8000 HANGING DROP, TEMPERATURE 291K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.158	α = 90
b = 81.635	β = 107.47
c = 65.31	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	MARRESEARCH		2002-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

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	2.2	29.1	96	0.12	9.7	3.1		25005

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	2.2	2.28	97		0.35	4.1	3

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	2.2	62.02	23736	1267	95.8	0.191	0.188	0.19	0.244	0.24	RANDOM	33.81

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]
-0.04		1.17	0.01		0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.788
r_scangle_it	2.842
r_scbond_it	1.711
r_angle_refined_deg	1.259
r_mcangle_it	1.117
r_angle_other_deg	0.815
r_mcbond_it	0.611
r_symmetry_vdw_other	0.295
r_nbd_other	0.245
r_nbd_refined	0.18
r_xyhbond_nbd_refined	0.178
r_symmetry_hbond_refined	0.167
r_symmetry_vdw_refined	0.109
r_chiral_restr	0.081
r_nbtor_other	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3191
Nucleic Acid Atoms
Solvent Atoms	342
Heterogen Atoms	19

Software

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