Experiment: 8BFD

Racemic structure of PK-7 (310HD-U2U5)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.12M Ethylene glycols, 0.1M (1.0M, pH 8.5 Tris (base); BICINE), 30% v/v (40% v/v PEG 500* MME; 20 % w/v PEG 20000)

Crystal Properties
Matthews coefficient	Solvent content
1.71	28.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 21.23	α = 105.85
b = 21.905	β = 112.44
c = 26.521	γ = 95.26

Symmetry
Space Group	P 1

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		2022-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9795	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	23.1	98.75	0.056	0.997	23.29	3.7		2744

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	2.072	99.26		0.1358	0.993	10.42	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	AB INITIO PHASING	THROUGHOUT	2	23.1	2475	317	99.79	0.2089	0.2029	0.2043	0.2564	0.2702	RANDOM	13.597

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]
0.83	-0.77	0.72	0.07	-0.12	-0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.042
r_dihedral_angle_3_deg	14.161
r_dihedral_angle_1_deg	5.917
r_angle_refined_deg	1.593
r_angle_other_deg	0.65
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	430
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	11

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Arcimboldo	phasing