7D7S | pdb_00007d7s

HIV-1 SF2 Nef in complex with the Fyn SH3 R96I mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4D8D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
2	VAPOR DIFFUSION, SITTING DROP	4.5	293	0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000
3	VAPOR DIFFUSION, SITTING DROP	4.5	293	0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.97
2.32	46.97
2.32	46.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.11	α = 90
b = 122.11	β = 90
c = 145.89	γ = 120

Symmetry
Space Group	P 64 2 2

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 EIGER2 X 9M	focusing bimorph mirrors in Kirkpatrick-Baez (KB) configuration	2020-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.98011	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	3.32	48.68	94.6	0.218	0.219	0.018	1	33.6	155.4		9209

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.324	3.46	42.1		9.136	9.163	0.71	0.486	1.1	165.4

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	4d8d	3.32	48.68	8283	923	92.24	0.28763	0.28616	0.28	0.29953	0.3	RANDOM	150.582

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]
0.98	0.49		0.98		-3.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.738
r_dihedral_angle_3_deg	19.364
r_dihedral_angle_4_deg	16.445
r_dihedral_angle_1_deg	6.355
r_angle_refined_deg	1.203
r_angle_other_deg	1.003
r_chiral_restr	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2737
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
XSCALE	data scaling
MOLREP	phasing