8AND | pdb_00008and

Domain swapped dimer of smolstatin (stefin) from Sphaerospora molnari

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	0.1 M calcium chloride dihydrate, 20% w/v PEG 6000, 10% v/v ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.508	α = 90
b = 97.867	β = 101.914
c = 38.626	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M		2021-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.99	37.79	98.48	0.07964	0.997	13.6	6.8		14976

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.991	2.062			0.933

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	AlphaFold	1.991	37.79	14975	749	98.507	0.201	0.1987	0.2	0.2452	0.25	41.327

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]
2.993		2.911	-4.583		0.331

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.428
r_dihedral_angle_4_deg	23.816
r_dihedral_angle_3_deg	15.524
r_lrange_other	7.154
r_lrange_it	7.142
r_dihedral_angle_1_deg	6.682
r_scangle_it	5.716
r_scangle_other	5.714
r_mcangle_it	4.619
r_mcangle_other	4.617
r_scbond_it	3.976
r_scbond_other	3.973
r_mcbond_it	3.363
r_mcbond_other	3.353
r_angle_other_deg	1.442
r_angle_refined_deg	1.32
r_xyhbond_nbd_refined	0.266
r_symmetry_nbd_refined	0.23
r_nbd_refined	0.217
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_other	0.175
r_nbd_other	0.12
r_symmetry_xyhbond_nbd_refined	0.099
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.06
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1451
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	16

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHENIX	phasing