3DS0 | pdb_00003ds0

HIV-1 capsid C-terminal domain mutant (N183A) in complex with an inhibitor of particle assembly (CAI)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BUO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	4.2	298	32% PEG 4000, 100mM ammonium acetate pH4.2, 10mM MgCl2, EVAPORATION, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.838	α = 90
b = 42.838	β = 90
c = 90.495	γ = 90

Symmetry
Space Group	P 41 21 2

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 225 mm CCD	Dynamically bendable mirror	2007-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.044	SLS	X06SA

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	38.7	99.4	0.079	0.079	25.6	13.9		11638			22.9

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)
	1.6	1.66	100		0.362	0.362	7.2	10.9	1140

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2BUO	1.6	38.72	11638	11086	551	99.22	0.20825	0.20636	0.21	0.24545	0.25	RANDOM	24.294

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			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.649
r_dihedral_angle_4_deg	13.558
r_dihedral_angle_3_deg	11.926
r_dihedral_angle_1_deg	4.528
r_scangle_it	4.069
r_sphericity_free	3.972
r_scbond_it	2.791
r_sphericity_bonded	2.44
r_mcangle_it	1.846
r_rigid_bond_restr	1.705
r_angle_refined_deg	1.305
r_mcbond_it	1.184
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.254
r_nbd_refined	0.204
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	733
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
RemDAq	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing