3DS4 | pdb_00003ds4

HIV-1 capsid C-terminal domain mutant (L211S) 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	PDB entry 2BUO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		298	PEG4000, 200mM ammonium sulfate, EVAPORATION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.51	α = 90
b = 69.27	β = 97.66
c = 41.55	γ = 90

Symmetry
Space Group	P 1 21 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 225 mm CCD		2007-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0080	ESRF	ID23-1

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	1.12	41.2	93.2	0.048	0.048	14.4	3.8		63254

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)
	1.12	1.19	73.3		0.41	0.41	2.4	5.6

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 2BUO	1.12	35.4	62969	2022	95.84	0.20907	0.20827	0.21	0.23412	0.24	RANDOM	17.054

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.83
r_dihedral_angle_4_deg	14.197
r_dihedral_angle_3_deg	11.544
r_dihedral_angle_1_deg	4.238
r_scangle_it	2.65
r_sphericity_free	2.49
r_scbond_it	2.256
r_sphericity_bonded	2.135
r_rigid_bond_restr	1.994
r_mcangle_it	1.364
r_angle_refined_deg	1.072
r_mcbond_it	0.923
r_nbtor_refined	0.3
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.118
r_symmetry_hbond_refined	0.109
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
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	1303
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
RemDAq	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing