1GZL | pdb_00001gzl

Crystal structure of C14linkmid/IQN17: a cross-linked inhibitor of HIV-1 entry bound to the gp41 hydrophobic pocket

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		UNBOUND IQN17 AND A MODEL OF C14LINKMID BOUND TO THE HYDROPHOBIC POCKET

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.6		16% ISOPROPANOL, 0.1 M TRIS, PH 8.6, 1 M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.358	α = 90
b = 38.358	β = 90
c = 169.695	γ = 120

Symmetry
Space Group	P 63

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 CCD		2000-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A		NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.8	20	91.9	0.044	13.6	5		59821			26.9

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	1.8	1.86	69.5		0.187	7.2	2.1

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	UNBOUND IQN17 AND A MODEL OF C14LINKMID BOUND TO THE HYDROPHOBIC POCKET	1.8	19.58	10672	685	81.7	0.208	0.208	0.2	0.243	0.25	RANDOM	36

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

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	15.9
c_scangle_it	3.3
c_mcangle_it	2.3
c_scbond_it	2.13
c_mcbond_it	1.4
c_angle_deg	1
c_improper_angle_d	0.67
c_bond_d	0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1002
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	16

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing