6R8C | pdb_00006r8c

HIV capsid hexamer with IP5 ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ES8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		270	PEG 6K, 1M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.663	α = 90
b = 90.663	β = 90
c = 56.997	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	CCD	OXFORD SAPPHIRE CCD		2019-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.978	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.913	78.52	99.3	0.056	0.998	17.7	6.5		20758

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	1.98	90		0.62	0.883	2.6	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	6ES8	1.92	29.69	19575	972	98.96	0.19308	0.19111	0.2	0.23426	0.24	RANDOM	35.456

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]
-0.04	-0.02		-0.04		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.226
r_dihedral_angle_1_deg	23.408
r_dihedral_angle_4_deg	23.091
r_dihedral_angle_3_deg	15.556
r_long_range_B_refined	7.24
r_long_range_B_other	7.179
r_scangle_other	5.533
r_mcangle_it	4.393
r_mcangle_other	4.392
r_scbond_other	3.794
r_scbond_it	3.788
r_mcbond_it	3.275
r_mcbond_other	3.27
r_angle_refined_deg	1.652
r_angle_other_deg	1.409
r_chiral_restr	0.092
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1580
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing