4U1M | pdb_00004u1m

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

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	291	10% PEG 6000, 10mM magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.06	α = 90
b = 81.34	β = 90
c = 110.93	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	2012-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.18	55.47	99.1	0.053	0.022	0.999	17.5	7.1		150669

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	1.18	1.21	96		0.721	0.294	0.823	3	6.8	10692

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	4I4W	1.18	55.47	150583	7561	99	0.1631	0.1622	0.17	0.1802	0.18	RANDOM	18.044

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]
-0.02			-0.07		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.337
r_dihedral_angle_4_deg	20.17
r_dihedral_angle_3_deg	13.305
r_dihedral_angle_1_deg	6.583
r_angle_refined_deg	2.438
r_mcangle_it	1.575
r_mcbond_it	1.045
r_mcbond_other	1.045
r_angle_other_deg	1.026
r_chiral_restr	0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.337
r_dihedral_angle_4_deg	20.17
r_dihedral_angle_3_deg	13.305
r_dihedral_angle_1_deg	6.583
r_angle_refined_deg	2.438
r_mcangle_it	1.575
r_mcbond_it	1.045
r_mcbond_other	1.045
r_angle_other_deg	1.026
r_chiral_restr	0.134
r_bond_refined_d	0.024
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3173
Nucleic Acid Atoms
Solvent Atoms	555
Heterogen Atoms	128

Software

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

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.