6R0E | pdb_00006r0e

Structure of F11TCR in complex with DR1 MHC Class II presenting PKYVKQNTLKLAT

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	291	0.1 M Na Cacodylate, 0.2 M NH4 SO4, 15 % PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.28	α = 90
b = 184.9	β = 90
c = 50.2	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	PIXEL	DECTRIS PILATUS3 S 6M		2015-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97623	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.91	92.46	99.9	0.078	0.084	0.031	0.999	14.1	7.2		96543			39.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	1.96	99.9		1.26	1.354	0.491		7.4

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1FYT	1.91	92.45	96461	4763	99.905	0.207	0.2055	0.21	0.2332	0.24	49.547

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]
-0.331			-0.679		1.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.264
r_dihedral_angle_1_deg	18.656
r_dihedral_angle_4_deg	17.013
r_dihedral_angle_3_deg	15.772
r_dihedral_angle_other_3_deg	11.667
r_lrange_other	6.543
r_lrange_it	6.542
r_scangle_it	3.382
r_scangle_other	3.382
r_mcangle_it	2.556
r_mcangle_other	2.555
r_scbond_it	2.219
r_scbond_other	2.219
r_angle_refined_deg	1.709
r_mcbond_it	1.613
r_mcbond_other	1.613
r_angle_other_deg	1.316
r_symmetry_nbd_refined	0.265
r_nbd_other	0.215
r_nbd_refined	0.201
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.167
r_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6567
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	43

Software

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