8AHG

PAC-FragmentDEL: Photoactivated covalent capture of DNA encoded fragments for hit discovery

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	0.8M Na/K tartrate 0.1M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.43	48.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.822	α = 90
b = 61.822	β = 90
c = 180.79	γ = 90

Symmetry
Space Group	P 41 21 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 EIGER2 XE 16M		2021-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.885	58.496	95.3	0.09	0.092	0.018	1	22.7	26.4		27812

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	1.885	1.952	50.6		3.058	3.115	0.588	0.638	1	27.2

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	2BVA	1.885	58.496	27811	1387	94.908	0.181	0.1785	0.2265	38.439

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]
-0.051			-0.051		0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.742
r_dihedral_angle_6_deg	16.412
r_lrange_it	7.424
r_lrange_other	7.387
r_dihedral_angle_1_deg	7.183
r_dihedral_angle_2_deg	6.122
r_scangle_it	5.92
r_scangle_other	5.919
r_scbond_it	4.244
r_scbond_other	4.242
r_mcangle_it	4.159
r_mcangle_other	4.159
r_mcbond_it	3.397
r_mcbond_other	3.394
r_angle_refined_deg	1.539
r_angle_other_deg	0.524
r_symmetry_xyhbond_nbd_refined	0.279
r_nbd_refined	0.213
r_nbd_other	0.21
r_xyhbond_nbd_refined	0.204
r_symmetry_nbd_refined	0.204
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.17
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.078
r_symmetry_xyhbond_nbd_other	0.048
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2308
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
Coot	model building