5NMF | pdb_00005nmf

868 TCR in complex with HLA A02 presenting SLYNTIATL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BNU	2BNU, 2V2W
experimental model	PDB	2V2W	2BNU, 2V2W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1 M Sodium Cacodylate, pH 6.0, 15% PEG 4000, 0.2 M Ammonium Sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 207.59	α = 90
b = 84.71	β = 90
c = 112.12	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 315r		2010-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.89	34.38	100	0.151	10.9	7.9		45223			60.3

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	2.89	2.96	100		0.84	2.9	8.2

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	2BNU, 2V2W	2.89	112.12	42905	2277	99.91	0.19587	0.19278	0.2	0.25527	0.26	RANDOM	57.387

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]
4.12			-1.64		-2.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.662
r_dihedral_angle_3_deg	20.945
r_dihedral_angle_4_deg	19.232
r_dihedral_angle_1_deg	8.192
r_long_range_B_refined	3.599
r_long_range_B_other	3.581
r_angle_refined_deg	1.871
r_mcangle_it	1.399
r_mcangle_other	1.399
r_scangle_other	1.347
r_angle_other_deg	1.093
r_scbond_it	0.876
r_scbond_other	0.804
r_mcbond_it	0.782
r_mcbond_other	0.782
r_chiral_restr	0.11
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13280
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	154

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
xia2	data reduction
SCALA	data scaling
PHASER	phasing