8AHF

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
2.37	47.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.315	α = 90
b = 109.315	β = 90
c = 135.866	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	2.271	85.17	95.7	0.201	0.999	14.6	26.8		36587

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	2.271	2.353	52.8		3.536	0.59	1.2	27.7

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	3BEO	2.271	85.17	36587	1828	94.626	0.18	0.1772	0.18	0.2376	0.24	48.125

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]
-0.086			-0.086		0.172

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.92
r_dihedral_angle_6_deg	17.387
r_dihedral_angle_2_deg	13.97
r_lrange_it	12.478
r_lrange_other	12.474
r_scangle_it	10.331
r_scangle_other	10.005
r_scbond_it	7.706
r_scbond_other	7.45
r_mcangle_it	7.153
r_mcangle_other	7.152
r_dihedral_angle_1_deg	6.794
r_mcbond_it	5.533
r_mcbond_other	5.533
r_angle_refined_deg	1.639
r_angle_other_deg	0.559
r_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.197
r_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.191
r_symmetry_nbd_refined	0.189
r_nbd_other	0.167
r_nbtor_refined	0.162
r_chiral_restr	0.077
r_symmetry_nbtor_other	0.073
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5792
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	88

Software

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