4EMZ

HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch underoil	6.5	298	0.1M HEPES, 3% PEG8000, pH 6.5, Microbatch underoil, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.324	α = 90
b = 112.471	β = 90
c = 114.407	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	CCD			2010-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9792	APS	24-ID-E

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	2.9	40	99.9	0.114	8.8	6		26098

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	100			5.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.9	30	24623	1317	99.39	0.22543	0.22268	0.27795	RANDOM	117.856

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]
0.99			-2.48		1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.864
r_dihedral_angle_3_deg	22.35
r_dihedral_angle_4_deg	20.727
r_dihedral_angle_1_deg	8.078
r_angle_refined_deg	1.765
r_angle_other_deg	1.553
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.007
r_gen_planes_other	0.007
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6755
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction