4DEN | pdb_00004den

Structural insightsinto potent, specific anti-HIV property of actinohivin; Crystal structure of actinohivin in complex with alpha(1-2) mannobiose moiety of high-mannose type glycan of gp120

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A07	PDB ENTRY 3A07

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	298	20% w/v PEG 1000, 0.2M NaCl, 0.1M Na/K phosphate buffer pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.217	α = 90
b = 56.217	β = 90
c = 56.217	γ = 90

Symmetry
Space Group	P 21 3

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 210		2009-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.00	Photon Factory	AR-NW12A

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	1.6	39.75	99.5	0.06	20.1	19.4		8067

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	1.6	1.63	100		0.57	7.8	19.3	402

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	PDB ENTRY 3A07	1.6	39.75	7647	370	99.16	0.14721	0.14473	0.14	0.20167	0.2	RANDOM	16.958

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
r_dihedral_angle_2_deg	33.199
r_dihedral_angle_3_deg	15.246
r_dihedral_angle_4_deg	10.212
r_dihedral_angle_1_deg	6.728
r_scangle_it	3.779
r_scbond_it	2.922
r_angle_refined_deg	2.197
r_mcangle_it	1.809
r_mcbond_it	1.176
r_chiral_restr	0.153

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.199
r_dihedral_angle_3_deg	15.246
r_dihedral_angle_4_deg	10.212
r_dihedral_angle_1_deg	6.728
r_scangle_it	3.779
r_scbond_it	2.922
r_angle_refined_deg	2.197
r_mcangle_it	1.809
r_mcbond_it	1.176
r_chiral_restr	0.153
r_bond_refined_d	0.021
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	875
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	72

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.