8BC7 | pdb_00008bc7

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex an aminoglutarimide degron peptide

X-RAY DIFFRACTION

---

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, HANGING DROP		294	0.5 M (NH4)H2PO4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.606	α = 90
b = 59.45	β = 90
c = 89.059	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 S 16M		2022-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	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	1.719	49.446	100	0.104	0.999	12.2	13.05		32675

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	1.72	1.82	100		1.91	0.632	1.18	13.54

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	FOURIER SYNTHESIS	FREE R-VALUE	4V2Y	1.719	49.446	32675	1633	99.957	0.176	0.1743	0.19	0.2111	0.22	41.172

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]
-0.695			1.396		-0.701

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.414
r_dihedral_angle_4_deg	17.528
r_dihedral_angle_3_deg	13.195
r_dihedral_angle_1_deg	7.055
r_lrange_it	6.249
r_lrange_other	6.24
r_scangle_it	4.34
r_scangle_other	4.339
r_scbond_it	2.784
r_scbond_other	2.782
r_mcangle_it	2.623
r_mcangle_other	2.623
r_mcbond_it	1.789
r_mcbond_other	1.785
r_angle_refined_deg	1.76
r_angle_other_deg	1.458
r_symmetry_xyhbond_nbd_refined	0.387
r_nbd_refined	0.213
r_symmetry_nbd_other	0.204
r_xyhbond_nbd_refined	0.191
r_nbd_other	0.19
r_nbtor_refined	0.181
r_ncsr_local_group_3	0.143
r_ncsr_local_group_2	0.141
r_ncsr_local_group_1	0.125
r_chiral_restr	0.103
r_symmetry_nbd_refined	0.102
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2426
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	41

Software

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