1LP9 | pdb_00001lp9

Xenoreactive complex AHIII 12.2 TCR bound to p1049/HLA-A2.1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B0G	Class I MHC, PDB ENTRY 1B0G. TCR, PDB ENTRY 2CKB
experimental model	PDB	2CKB	Class I MHC, PDB ENTRY 1B0G. TCR, PDB ENTRY 2CKB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	PEG3350, 25mM MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.708	α = 90
b = 84.469	β = 92.13
c = 121.336	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	Bent Cylinder, 1:1 defocused rhodium-coated electroless nickel-plated bent aluminum cylinder	2001-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12B	1.01715	NSLS	X12B

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	30	99.9	0.074	28.5	7.5	122580	121366

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	2.05	99.9		0.578	3.5

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	Class I MHC, PDB ENTRY 1B0G. TCR, PDB ENTRY 2CKB	2	30	122580	121366	6421	99.99	0.23	0.22058	0.21887	0.23	0.25293	0.26	RANDOM	14.229

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]
1.18		0.98	0.59		-1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.406
r_dihedral_angle_1_deg	4.288
r_sphericity_free	3.612
r_scangle_it	2.228
r_scbond_it	1.507
r_angle_refined_deg	1.435
r_sphericity_bonded	1.083
r_mcangle_it	1.067
r_rigid_bond_restr	0.902
r_angle_other_deg	0.811
r_mcbond_it	0.658
r_symmetry_hbond_other	0.532
r_symmetry_hbond_refined	0.371
r_xyhbond_nbd_other	0.357
r_symmetry_vdw_refined	0.334
r_symmetry_vdw_other	0.328
r_nbd_refined	0.284
r_nbd_other	0.229
r_xyhbond_nbd_refined	0.188
r_chiral_restr	0.09
r_nbtor_other	0.065
r_gen_planes_other	0.049
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13136
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction