7M9F | pdb_00007m9f

Structure of the wild-type native full-length HIV-1 capsid protein in complex with ZW-1261

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	PEG 3350, NaI, Sodium Cacodylate, Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.9	α = 90
b = 90.9	β = 90
c = 56.14	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		2020-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.7	45.71	97.9	0.108	0.118	0.996	13.62	7.208		7239			69.356

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.77	91.1		0.768	0.84	0.783	3.39	6.064

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	4XFZ	2.7	45.71	6881	356	97.85	0.1728	0.1686	0.18	0.2533	0.26	RANDOM	70.635

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]
-0.36	-0.18		-0.36		1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	93.971
r_dihedral_angle_2_deg	37.735
r_dihedral_angle_4_deg	22.429
r_sphericity_bonded	20.046
r_dihedral_angle_3_deg	17.883
r_dihedral_angle_1_deg	7.009
r_rigid_bond_restr	4.978
r_angle_refined_deg	1.893
r_angle_other_deg	1.371
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	93.971
r_dihedral_angle_2_deg	37.735
r_dihedral_angle_4_deg	22.429
r_sphericity_bonded	20.046
r_dihedral_angle_3_deg	17.883
r_dihedral_angle_1_deg	7.009
r_rigid_bond_restr	4.978
r_angle_refined_deg	1.893
r_angle_other_deg	1.371
r_chiral_restr	0.098
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1725
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	38

Software

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

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.