Experiment: 9LQK

Crystal structure of synthetic ubiquitin variant R10 designed by ProteinMPNN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	0.2 M MgSO4, 8% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
1.73	28.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.556	α = 90
b = 62.548	β = 90
c = 89.757	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 EIGER2 X 16M		2024-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 07A	1	NSRRC	TPS 07A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.55	25.66	97.1	0.06	23.29	4.9		23160			22.63

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.606	90.8		0.416	2.63	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.55	25.66	1.34	23078	1130	96.62	0.1933	0.1914	0.1917	0.2287	0.2287	32.93

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.8857
f_angle_d	0.8995
f_chiral_restr	0.0568
f_plane_restr	0.0066
f_bond_d	0.0065

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1268
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHENIX	refinement
Coot	model building
Blu-Ice	data collection
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction