3FT2 | pdb_00003ft2

Crystal Structure of a citrulline peptide variant of the minor histocompatibility peptide HA-1 in complex with HLA-A2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	12-15% w/v PEG 6000, 0.1 M NaCl and 0.1 M tri-sodium-citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.56	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.369	α = 90
b = 80.104	β = 114.59
c = 57.985	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 315		2007-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.95	ESRF	ID23-1

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	1.8	50	96.2	0.068	16.1	5.5		40771			27.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	78.8		0.452	3.3	4.3	3097

Refinement

Statistics
Diffraction ID	Structure Solution Method	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	1.8	14.89	40771	40771	4078	100	0.18104	0.181	0.17854	0.18	0.21792	0.19	random	29.349

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.349
r_dihedral_angle_4_deg	16.805
r_dihedral_angle_3_deg	14.091
r_dihedral_angle_1_deg	5.85
r_scangle_it	3.191
r_mcangle_it	3.009
r_scbond_it	2.246
r_mcbond_it	2.156
r_angle_refined_deg	1.156
r_nbtor_refined	0.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.349
r_dihedral_angle_4_deg	16.805
r_dihedral_angle_3_deg	14.091
r_dihedral_angle_1_deg	5.85
r_scangle_it	3.191
r_mcangle_it	3.009
r_scbond_it	2.246
r_mcbond_it	2.156
r_angle_refined_deg	1.156
r_nbtor_refined	0.294
r_nbd_refined	0.19
r_symmetry_hbond_refined	0.159
r_symmetry_vdw_refined	0.137
r_xyhbond_nbd_refined	0.11
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3252
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.