4XRQ | pdb_00004xrq

Disulfide stabilized HIV-1 CA hexamer 4mut (S41A, Q67H, V165I, L172I) in complex with PF-3450074

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H47

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	0.2 M potassium thiocyanate, 8% w/v PEG 20K, 8% v/v PEG 550 MME, 0.1 M TRIS pH 8.5, 3% 1,4-dioxane

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.35	α = 90
b = 90.35	β = 90
c = 56.93	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	IMAGE PLATE	RIGAKU RAXIS HTC		2013-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.95	78.245	100	0.076	0.083	0.033	15.4	6.1	19460	19460

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.06	100		0.668	0.668	0.299	1.2	6	2842

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	3h47	1.95	39.12	18460	995	99.95	0.1906	0.189	0.1986	0.2212	0.2274	RANDOM	35.385

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]
0.38	0.19		0.38		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.645
r_dihedral_angle_4_deg	18.902
r_dihedral_angle_3_deg	11.642
r_dihedral_angle_1_deg	4.834
r_mcangle_it	4.678
r_mcbond_it	3.373
r_mcbond_other	3.369
r_angle_refined_deg	0.964
r_angle_other_deg	0.739
r_chiral_restr	0.053

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.645
r_dihedral_angle_4_deg	18.902
r_dihedral_angle_3_deg	11.642
r_dihedral_angle_1_deg	4.834
r_mcangle_it	4.678
r_mcbond_it	3.373
r_mcbond_other	3.369
r_angle_refined_deg	0.964
r_angle_other_deg	0.739
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1639
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	32

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
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.