4U1I | pdb_00004u1i

HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4I4W	homology model based on PDB entry 4I4W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	291	0.1 M HEPES pH 7.0, 20% PEG 4000 and 0.2 M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.25	α = 90
b = 81.49	β = 90
c = 110.14	γ = 90

Symmetry
Space Group	P 21 21 21

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	PSI PILATUS 6M	mirrors	2013-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.92	45.63	99.7	0.231	0.091	0.995	11.8	7.4		35895

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.97	99.8		1.454	0.563	0.745	3.7	7.6	2624

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	homology model based on PDB entry 4I4W	1.92	45.63	35838	1793	99.54	0.1782	0.1765	0.2075	0.2098	RANDOM	26.172

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]
0.05			-0.33		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.197
r_dihedral_angle_4_deg	19.048
r_dihedral_angle_3_deg	15.899
r_dihedral_angle_1_deg	6.811
r_mcangle_it	1.963
r_angle_refined_deg	1.915
r_mcbond_it	1.206
r_mcbond_other	1.206
r_angle_other_deg	0.932
r_chiral_restr	0.121
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3175
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms	35

Software

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