7N9X

CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		295	100 mM Bis-Tris propane, pH 6.8, 15% PEG3350, 200 mM sodium

Crystal Properties
Matthews coefficient	Solvent content
4.23	70.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.95	α = 90
b = 137.85	β = 90
c = 313.832	γ = 90

Symmetry
Space Group	I 2 2 2

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		2018-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.0711	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.5	50	95.9	0.182	0.216	0.114	5	3.3		33153

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.5	3.56	98.7		1.179	1.405	0.748	0.38		3.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entries 5O2U & 3H47	3.511	49.581	33142	1668	94.389	0.246	0.2449	0.2699	180.204

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]
0.4			2.014		-2.414

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.926
r_lrange_it	19.575
r_dihedral_angle_4_deg	15.919
r_dihedral_angle_3_deg	14.578
r_mcangle_it	11.904
r_scangle_it	11.721
r_scbond_it	7.575
r_mcbond_it	7.218
r_dihedral_angle_1_deg	5.008
r_angle_refined_deg	1.602
r_symmetry_xyhbond_nbd_refined	0.39
r_nbtor_refined	0.321
r_symmetry_nbd_refined	0.314
r_nbd_refined	0.232
r_ncsr_local_group_5	0.231
r_ncsr_local_group_6	0.22
r_ncsr_local_group_8	0.196
r_ncsr_local_group_4	0.194
r_xyhbond_nbd_refined	0.19
r_ncsr_local_group_9	0.184
r_ncsr_local_group_7	0.18
r_ncsr_local_group_1	0.158
r_ncsr_local_group_2	0.158
r_ncsr_local_group_3	0.152
r_ext_dist_refined_d	0.094
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11458
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
PHASER	phasing