4U1S | pdb_00004u1s

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	8	291	0.2 M Lithium Chloride, pH 8, 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.17	α = 90
b = 81.25	β = 90
c = 110.77	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	2011-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.76	40.625	100	0.096	0.109	0.038	16.1	7.9	46617	46617

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.76	1.81	100		1.014	1.014	0.396	0.6	8	3399

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	1.76	40.62	46542	2350	99.94	0.1766	0.175	0.18	0.2067	0.21	RANDOM	27.041

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]
0.29			-0.13		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.396
r_dihedral_angle_4_deg	17.142
r_dihedral_angle_3_deg	14.959
r_dihedral_angle_1_deg	6.811
r_mcangle_it	2.218
r_angle_refined_deg	1.961
r_mcbond_other	1.411
r_mcbond_it	1.41
r_angle_other_deg	0.95
r_chiral_restr	0.138

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.396
r_dihedral_angle_4_deg	17.142
r_dihedral_angle_3_deg	14.959
r_dihedral_angle_1_deg	6.811
r_mcangle_it	2.218
r_angle_refined_deg	1.961
r_mcbond_other	1.411
r_mcbond_it	1.41
r_angle_other_deg	0.95
r_chiral_restr	0.138
r_bond_refined_d	0.019
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	3185
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	59

Software

Software
Software Name	Purpose
XDS	data reduction
SCALA	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.