8V17 | pdb_00008v17

HIV-CA Disulfide linked Hexamer with inhibitor bound - exploration of a benzothiazole

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8TOV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Morpheus Condition D11

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.902	α = 90
b = 90.902	β = 90
c = 56.468	γ = 120

Symmetry
Space Group	P 6

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 EIGER X 16M		2023-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95372	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.5	45.927	100	0.041	0.999	14.8	41.7		42672

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	100		1.184	0.615	1.4	42.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	45.927	42665	2080	99.986	0.144	0.142	0.142	0.1714	0.1715	27.094

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]
-0.106	-0.053		-0.106		0.342

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	19.509
r_lrange_other	19.123
r_dihedral_angle_6_deg	16.471
r_scangle_it	14.859
r_scangle_other	14.854
r_dihedral_angle_2_deg	14.547
r_dihedral_angle_3_deg	13.012
r_mcangle_other	12.619
r_mcangle_it	12.617
r_scbond_it	10.727
r_scbond_other	10.722
r_mcbond_it	8.709
r_mcbond_other	8.662
r_dihedral_angle_1_deg	5.903
r_rigid_bond_restr	4.788
r_angle_refined_deg	1.871
r_angle_other_deg	0.672
r_symmetry_xyhbond_nbd_refined	0.356
r_nbd_refined	0.234
r_symmetry_nbd_refined	0.216
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.181
r_nbd_other	0.167
r_chiral_restr	0.108
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.037
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_chiral_restr_other	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1676
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	55

Software

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