7Q9B | pdb_00007q9b

MHC Class I A02 Allele presenting EAAGIGILTV, in complex with Mel8 TCR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.972	α = 90
b = 53.645	β = 94.333
c = 203.507	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	PIXEL	DECTRIS EIGER2 X 16M		2019-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	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	3.24	99.7	100	0.28	0.328	0.22	0.995	2.7	3.7		34992			36.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.24	3.32	99.9		0.949	1.102	0.719	0.686		3.8

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	3HG1	3.24	99.686	34983	1742	99.894	0.229	0.2264	0.23	0.2765	0.27	56.356

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]
-0.525		-0.611	-1.764		2.355

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.518
r_dihedral_angle_3_deg	19.074
r_dihedral_angle_4_deg	16.531
r_dihedral_angle_1_deg	8.226
r_angle_refined_deg	1.452
r_lrange_it	1.266
r_lrange_other	1.266
r_angle_other_deg	1.126
r_symmetry_xyhbond_nbd_refined	0.269
r_symmetry_nbd_refined	0.246
r_nbd_other	0.243
r_nbd_refined	0.21
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.169
r_ncsr_local_group_3	0.166
r_xyhbond_nbd_refined	0.16
r_ncsr_local_group_4	0.147
r_ncsr_local_group_2	0.111
r_ncsr_local_group_1	0.104
r_mcangle_it	0.081
r_mcangle_other	0.081
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.054
r_mcbond_it	0.043
r_mcbond_other	0.043
r_scangle_it	0.042
r_scangle_other	0.042
r_symmetry_xyhbond_nbd_other	0.034
r_scbond_it	0.022
r_scbond_other	0.022
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13160
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	8

Software

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