7QDF | pdb_00007qdf

Hexameric HIV-1 (M-group) CA R120 mutant

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	293	9.5% PEG 3350 (v/v), 310 mM NaI, 100 mM Sodium Cacodylate. Crystals grew in 1 uL protein (3 mg/mL) + 1 uL crystallant. Cryoprotected in 20% (v/v) Glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.36	α = 90
b = 92.36	β = 90
c = 57.44	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 EIGER R 4M		2020-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	1.0332	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.304	79.98	98.4	0.071	0.997	10.76	3.9		12346

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	2.304	2.44			0.503	1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4XFX	2.304	46.656	12276	578	98.397	0.244	0.2423	0.24	0.2775	0.29	93.332

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]
-5.699			-5.699		11.398

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.959
r_dihedral_angle_4_deg	24.062
r_dihedral_angle_3_deg	20.023
r_lrange_it	14.589
r_scangle_it	9.558
r_mcangle_it	8.903
r_scbond_it	6.813
r_mcbond_it	6.147
r_dihedral_angle_1_deg	5.43
r_angle_refined_deg	2.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.959
r_dihedral_angle_4_deg	24.062
r_dihedral_angle_3_deg	20.023
r_lrange_it	14.589
r_scangle_it	9.558
r_mcangle_it	8.903
r_scbond_it	6.813
r_mcbond_it	6.147
r_dihedral_angle_1_deg	5.43
r_angle_refined_deg	2.017
r_symmetry_xyhbond_nbd_refined	0.449
r_symmetry_nbd_refined	0.405
r_nbtor_refined	0.331
r_nbd_refined	0.301
r_xyhbond_nbd_refined	0.235
r_chiral_restr	0.141
r_gen_planes_refined	0.01
r_bond_refined_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1723
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	11

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.