Experiment: 9L8Y

Crystal structure of HERC2

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	8.8	289	0.02 M Citric acid, 0.08 M BIS-TRIS propane (pH 8.8), 16% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.232	α = 90
b = 99.591	β = 90
c = 123.297	γ = 90

Symmetry
Space Group	F 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 EIGER X 16M		2022-01-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97856	SSRF	BL10U2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	1.92	49.8	99.9	0.026	15.2	9.1		14962			39.08

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.96			0.356

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	1.92	28.13	1.36	14952	713	99.87	0.181	0.1797	0.1794	0.2061	0.2055	53.61

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	6.3337
f_angle_d	1.4109
f_chiral_restr	0.0858
f_plane_restr	0.0132
f_bond_d	0.0121

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1219
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing