8C3H

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex a long aspartimide degron peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4V2Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		274	0.5 M (NH4)H2PO4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.256	α = 90
b = 58.821	β = 90
c = 88.858	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 EIGER2 X 16M		2022-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9998	SLS	X10SA

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	1.71	47.53	99.7	0.082	1	14.3	12.84		32554

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.71	1.81	98.8		1.629	0.701	1.15	12.42

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	4V2Y	1.71	47.53	32553	1630	99.7	0.181	0.1794	0.2104	40.02

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]
-1.69			2.273		-0.584

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.683
r_dihedral_angle_4_deg	20.201
r_dihedral_angle_3_deg	12.508
r_dihedral_angle_1_deg	6.9
r_lrange_it	5.695
r_lrange_other	5.67
r_scangle_it	3.84
r_scangle_other	3.839
r_mcangle_it	2.544
r_mcangle_other	2.543
r_scbond_it	2.504
r_scbond_other	2.504
r_mcbond_it	1.829
r_mcbond_other	1.829
r_angle_refined_deg	1.769
r_angle_other_deg	1.451
r_nbd_refined	0.241
r_nbd_other	0.22
r_symmetry_nbd_other	0.206
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.158
r_symmetry_nbd_refined	0.109
r_ncsr_local_group_1	0.107
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.055
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2139
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling