Experiment: 10YL

Crystal structure of a computationally designed protein, dnMSBP, apo form

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		296	700 uM dnMSBP in 25 mM Tris buffer at pH 8 containing 300 mM NaCl was mixed with 200 mM ammonium phosphate monobasic buffer at pH 4.6 with 20% w/v PEG 3350 at a 1:1 mixing ratio under room temperature

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.484	α = 90
b = 119.484	β = 90
c = 119.484	γ = 90

Symmetry
Space Group	I 2 3

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 PILATUS3 6M		2022-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

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	2.19	42.24	99.97	0.1079	0.1105	0.02337	0.999	15.94	22.3		14768			49.98

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	2.19	2.269			1.498	1.533	0.3247	0.799	1.18

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	2.19	42.24	1.38	14767	1357	100	0.2157	0.2135	0.2206	0.2617	0.2673	53.51

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	5.1034
f_angle_d	0.2805
f_chiral_restr	0.0267
f_plane_restr	0.0018
f_bond_d	0.0013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1539
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	33

Software

Software
Software Name	Purpose
JBluIce-EPICS	data collection
xia2	data scaling
xia2	data reduction
PHENIX	phasing
PHENIX	refinement