Experiment: 9RPC

HIV-1 capsid (M-group) - native

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XFX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	9.5-11% PEG 3350 (v/v), 250-350 mM NaI, 100 mM Sodium Cacodylate [pH 6.5]. Crystals grew in 1 uL protein (3 mg/mL) + 1 uL crystallant. Cryoprotected in 20% (v/v) Glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.46	α = 90
b = 92.46	β = 90
c = 57.76	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		2019-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.97625	EMBL/DESY, HAMBURG	X13

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	1.97	80.07	92.4	0.13	0.991	12.2	19.1		18549

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2			0.396

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.969	80.07	18541	997	92.3	0.2352	0.2329	0.259	0.278	0.271	RANDOM	59.64

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]
-2.1243			-2.1243		4.2486

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.23
t_omega_torsion	2.94
t_angle_deg	0.97
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_sum_occupancies
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1725
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	12

Software

Software
Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing