5JPA | pdb_00005jpa

Hexameric HIV-1 CA H12Y mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H47

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	290	PEG 550MME (12% w/v), KSCN (0.15M), 0.1M TRIS

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.6	α = 90
b = 90.6	β = 90
c = 56.931	γ = 120

Symmetry
Space Group	P 6

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2014-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9794	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.7	56.93	95.1	0.095	0.105	0.043	0.992	9	4.8		27756

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	94.7		0.813		4.9

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	3H47	1.7	56.93	26370	1379	94.27	0.199	0.1971	0.206	0.232	0.2062	RANDOM	27.491

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]
0.24	0.12		0.24		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.619
r_dihedral_angle_4_deg	18.225
r_dihedral_angle_3_deg	11.5
r_dihedral_angle_1_deg	4.83
r_mcangle_it	3.405
r_mcbond_it	2.194
r_mcbond_other	2.184
r_angle_refined_deg	1.009
r_angle_other_deg	0.843
r_chiral_restr	0.06
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1609
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction