3PGD | pdb_00003pgd

Crystal Structure of HLA-DR1 with CLIP106-120, canonical peptide orientation

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	PEG 3350, NaCitrate, BisTris propane, pH 6.5, vapor diffusion, sitting drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.449	α = 90
b = 94.449	β = 90
c = 275.535	γ = 90

Symmetry
Space Group	P 43 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	Rayonix		2010-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	2.72	35	99.9	0.131	12.19		34529	34493		-3	45.618

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)
	2.72	2.79	100		0.873	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	2.72	33.393	2	34451	1725	99.86	0.1983	0.196	0.1934	0.2416	0.2375	RANDOM	44.5183

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]
3.4245			3.4245		-6.8491

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.141
f_angle_d	1.132
f_chiral_restr	0.07
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6151
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection