8VRP | pdb_00008vrp

HIV-CA Disulfide linked Hexamer bound to 4-Quinazolinone Scaffold inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8V17

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Morpheus condition B2

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.268	α = 90
b = 160.268	β = 90
c = 57.235	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		2023-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95373	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	1.8	46.618	100	0.049	0.998	13	42.3		78027

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	1.8	1.84	100		2.231	0.441	1	43.1

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	1.8	46.618	78025	3905	99.991	0.194	0.1924	0.2005	0.2257	0.2332	33.799

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]
-0.022	-0.011		-0.022		0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.744
r_dihedral_angle_other_2_deg	27.148
r_dihedral_angle_6_deg	16.713
r_dihedral_angle_3_deg	12.808
r_lrange_it	8.32
r_lrange_other	8.289
r_scangle_it	6.995
r_scangle_other	6.994
r_dihedral_angle_1_deg	5.852
r_scbond_it	4.591
r_scbond_other	4.59
r_mcangle_it	4.56
r_mcangle_other	4.56
r_mcbond_it	3.243
r_mcbond_other	3.24
r_angle_refined_deg	1.752
r_angle_other_deg	0.605
r_symmetry_xyhbond_nbd_refined	0.275
r_nbd_refined	0.234
r_nbd_other	0.212
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.182
r_symmetry_nbd_refined	0.154
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.074
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_chiral_restr_other	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5096
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	205

Software

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