8AHE

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BEO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	292	0.2 M Ammonium sulfate 50 mM BIS-TRIS pH 5.6 28% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.119	α = 90
b = 109.119	β = 90
c = 136.207	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		2021-11-27	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)	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	2.108	85.161	95.6	0.216	0.999	13.7	26.8		39374

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	2.108	2.285	58.7		2.657	0.582	1.5	25.5

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	3BEO	2.108	85.161	39374	1989	81.906	0.187	0.1844	0.2347	44.579

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]
0.005			0.005		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.356
r_dihedral_angle_6_deg	17.429
r_lrange_it	11.791
r_lrange_other	11.774
r_scangle_it	9.727
r_scangle_other	9.505
r_dihedral_angle_2_deg	7.328
r_scbond_it	7.192
r_scbond_other	7.026
r_dihedral_angle_1_deg	6.712
r_mcangle_it	6.614
r_mcangle_other	6.614
r_mcbond_it	5.108
r_mcbond_other	5.108
r_angle_refined_deg	1.632
r_angle_other_deg	0.561
r_symmetry_nbd_refined	0.226
r_nbd_refined	0.214
r_symmetry_nbd_other	0.191
r_xyhbond_nbd_refined	0.183
r_nbd_other	0.183
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.155
r_chiral_restr_other	0.089
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.074
r_symmetry_xyhbond_nbd_other	0.046
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5779
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	64

Software

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