Experiment: 9Q88

High-resolution structure of RNF38 RING domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4V3K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	Molecular Dimensions; 0.09 M Halogens, 0.1 M Buffer System 1 pH 6.5, 37.5 % v/v Precipitant Mix 4

Crystal Properties
Matthews coefficient	Solvent content
1.82	82.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.82	α = 90
b = 39.309	β = 90
c = 53.208	γ = 90

Symmetry
Space Group	P 21 21 21

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		2019-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.97950	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.2	31.62	80.04	0.053	0.026	0.999	18.1	5.3		30264			10.24

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.28			0.27	0.51	0.937	1.9

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.2	31.62	1.34	30264	1411	74.99	0.152	0.1512	0.1684	0.1609	RANDOM	18.2

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	6.2967
f_angle_d	1.2132
f_chiral_restr	0.0923
f_bond_d	0.0103
f_plane_restr	0.0082

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	635
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHENIX	phasing