3DS5 | pdb_00003ds5

HIV-1 capsid C-terminal domain mutant (N183A)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A80	PDB entry 1A80

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	4.6	298	30% PEG 4000, 100mM ammonium acetate, 10mM MgCl2, pH 4.6, EVAPORATION, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.359	α = 109.2
b = 51.321	β = 109.63
c = 51.358	γ = 109.55

Symmetry
Space Group	P 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	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	2.4	42	86.3	0.025	0.025	36.4	3.1		13571			61.8

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)
	2.4	2.49	43.6		0.139	0.139	5	2.2	692

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 1A80	2.4	41.96	12892	677	85.94	0.22269	0.22015	0.22	0.26977	0.26	RANDOM	60.251

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]
1.68	0.78	0.77	-0.81	-1.57	-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.755
r_dihedral_angle_4_deg	23.891
r_dihedral_angle_3_deg	20.618
r_dihedral_angle_1_deg	6.339
r_scangle_it	3.761
r_scbond_it	2.301
r_angle_refined_deg	1.617
r_mcangle_it	1.427
r_mcbond_it	0.809
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.227
r_symmetry_hbond_refined	0.21
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.092
r_bond_refined_d	0.014
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2292
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms

Software

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