4END

Crystal structure of anti-HIV actinohivin in complex with alpha-1,2-mannobiose (P 2 21 21 form)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.2M Ammonium phosphate, 0.1M Tris, 50% (v/v) 2-Methyl-2,4-pentanediol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.84	α = 90
b = 66.84	β = 90
c = 67.06	γ = 90

Symmetry
Space Group	P 2 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2012-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.00	Photon Factory	BL-5A

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	1.9	27.84	99.9	0.111	11.2	6.5		10409

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)
1	1.9	2	100		0.348	4.6	6.6	1483

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4DEN	1.9	25.7	10409	9805	497	99.13	0.16703	0.16382	0.23094	RANDOM	15.345

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]
0.01			-0.02		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.854
r_dihedral_angle_4_deg	16.195
r_dihedral_angle_3_deg	12.762
r_dihedral_angle_1_deg	6.442
r_scangle_it	4.456
r_scbond_it	3.121
r_mcangle_it	1.947
r_angle_refined_deg	1.908
r_mcbond_it	1.191
r_chiral_restr	0.144

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.854
r_dihedral_angle_4_deg	16.195
r_dihedral_angle_3_deg	12.762
r_dihedral_angle_1_deg	6.442
r_scangle_it	4.456
r_scbond_it	3.121
r_mcangle_it	1.947
r_angle_refined_deg	1.908
r_mcbond_it	1.191
r_chiral_restr	0.144
r_bond_refined_d	0.022
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	886
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	75

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.