3VQ7 | pdb_00003vq7

HIV-1 IN core domain in complex with 4-(1H-pyrrol-1-yl)aniline

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3L3U	PDB ENTRY 3l3u

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	295	1.6M AmSO4, 0.1M Na Citrate pH 5.6, 50mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.284	α = 90
b = 61.658	β = 90
c = 82.017	γ = 90

Symmetry
Space Group	P 21 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 210r	Mirror	2007-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.95363	Australian Synchrotron	MX1

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	1.6	34.15	99.57	0.08	0.09	15.2	7.2	38588	38422	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.634	1.692	95.74

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 3l3u	1.63	34.15	38588	36498	1924	99.46	0.199	0.20042	0.199	0.21	0.22677	0.23	RANDOM	20.482

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]
-0.33			1.43		-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.937
r_dihedral_angle_3_deg	14.657
r_dihedral_angle_4_deg	13.073
r_dihedral_angle_1_deg	5.987
r_scangle_it	3.293
r_scbond_it	2.293
r_angle_refined_deg	1.749
r_mcangle_it	1.715
r_mcbond_it	1.202
r_angle_other_deg	0.959
r_symmetry_vdw_other	0.29
r_mcbond_other	0.241
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.2
r_nbd_other	0.199
r_metal_ion_refined	0.19
r_symmetry_hbond_refined	0.181
r_symmetry_vdw_refined	0.177
r_nbtor_refined	0.176
r_chiral_restr	0.086
r_nbtor_other	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2190
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	61

Software

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