6EQA | pdb_00006eqa

HLA class I histocompatibility antigen

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		291	0.1 M HEPES pH 7.5, 25% PEG 4000 and 15% glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.4	α = 90
b = 121.4	β = 90
c = 82.32	γ = 90

Symmetry
Space Group	P 43

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 PILATUS 2M		2011-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9173	Diamond	I04-1

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	3.16	82.32	100	0.119	13.4	6.6		20733

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)
1	3.16	3.24	100		0.727		6.9

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	3HG1	3.16	68.13	19653	1062	100	0.1896	0.1856	0.1875	0.263	0.2512	RANDOM	58.181

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]
1.35			1.35		-2.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.234
r_dihedral_angle_3_deg	20.579
r_dihedral_angle_4_deg	18.958
r_dihedral_angle_1_deg	8.358
r_angle_refined_deg	1.431
r_angle_other_deg	0.875
r_chiral_restr	0.08
r_bond_refined_d	0.013
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	6572
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
xia2	data reduction