1K5M

Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RHV	Wild-type HRV14 structure coordinates (PDB entry 4RHV)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 318.9	α = 90
b = 349.3	β = 90
c = 368.4	γ = 90

Symmetry
Space Group	I 2 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	108	CCD	NONIUS CAD4	mirror	1998-02-01	M	SINGLE WAVELENGTH
2	1	x-ray	108	CCD	ADSC QUANTUM 4	mirror	1998-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.10	NSLS	X25
2	SYNCHROTRON	CHESS BEAMLINE F1	0.92	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.7	50	92.8	0.114	10	13.8	513239	513239			29

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.8	82.7		0.212	4	5	46826

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	The free R-factor was calculated in early stages of model building and refinement to monitor the progress. Due to the strong interdependency of structure factors in the presence of high NCS, the free R-factor did not provide any useful information. Therefore, in the later stages of structure refinement, all data were included and no free R factor was calculated.	Wild-type HRV14 structure coordinates (PDB entry 4RHV)	2.7	50	2	513239	494360		89	0.216	0.216	0.22		18.4

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	26.7
x_improper_angle_d	1.7
x_angle_deg	1
x_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6459
Nucleic Acid Atoms
Solvent Atoms	637
Heterogen Atoms	21

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

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.