6UJ9 | pdb_00006uj9

Crystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide in complex with Fab

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6DF0	6DF0, 6UJ7
experimental model	PDB	6UJ7	6DF0, 6UJ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.5	292	0.1 M CHES, 20% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.605	α = 90
b = 42.006	β = 92.75
c = 125.18	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 9M		2019-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9201	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.9	48.93	98.1	0.15	0.18	0.98	6.48	3.104		19451			34.323

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.98	96.4		0.561	0.678	0.711	2.03	2.954

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	6DF0, 6UJ7	2.9	48.93	18480	973	98.15	0.2173	0.2137	0.2224	0.2868	0.2863	RANDOM	41.378

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]
2		-1.18	0.56		-2.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.74
r_dihedral_angle_3_deg	21.901
r_dihedral_angle_4_deg	19.107
r_dihedral_angle_1_deg	5.951
r_angle_refined_deg	1.539
r_angle_other_deg	1.306
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6460
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	95

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction