3VQ9 | pdb_00003vq9

HIV-1 IN core domain in complex with 6-fluoro-1,3-benzothiazol-2-amine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BL3	PDB ENTRY 1bl3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	0.4M SODIUM CITRATE, 50mM HEPES PH 7.5, 7.5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.327	α = 90
b = 72.909	β = 108.6
c = 79.851	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARMOSAIC 300 mm CCD		2007-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.94937	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	75.6	99.52	0.051	0.051	17.5	3.7	42674	42469	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	99.6		0.299	0.299	2.5

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 (All)	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 1bl3	1.9	75.59	42469	40326	2143	99.52	0.1958	0.1976	0.19578	0.2	0.23202	0.24	RANDOM	27.056

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]
1.77		0.55	-0.04		-1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.579
r_dihedral_angle_4_deg	14.37
r_dihedral_angle_3_deg	13.052
r_dihedral_angle_1_deg	4.949
r_scangle_it	4.535
r_angle_other_deg	4.118
r_scbond_it	3.004
r_mcangle_it	2.141
r_mcbond_it	1.243
r_angle_refined_deg	1.144
r_nbd_other	0.255
r_symmetry_vdw_other	0.232
r_nbd_refined	0.213
r_nbtor_refined	0.187
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.138
r_symmetry_vdw_refined	0.112
r_nbtor_other	0.11
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_other	0.005
r_gen_planes_refined	0.003
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3419
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	11

Software

Software
Software Name	Purpose
Blu-Ice	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling