8AOP

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 14r

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.4M Ammonium Phosphate

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.79	α = 90
b = 59.194	β = 90
c = 87.861	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		2021-07-10	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	1.94	47.7	100	0.048	1	19.51	6.93		22417

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	1.94	2.06	99.9		0.979	0.733	1.7	6.99

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	1.944	47.7	22417	1119	99.947	0.198	0.1967	0.2272	52.323

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]
0.283			1.195		-1.478

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.335
r_dihedral_angle_3_deg	11.744
r_dihedral_angle_4_deg	10.777
r_dihedral_angle_1_deg	6.677
r_lrange_it	4.398
r_lrange_other	4.397
r_scangle_it	2.918
r_scangle_other	2.917
r_mcangle_it	2.195
r_mcangle_other	2.194
r_scbond_it	1.845
r_scbond_other	1.845
r_angle_refined_deg	1.496
r_mcbond_other	1.413
r_mcbond_it	1.412
r_angle_other_deg	1.232
r_nbd_other	0.221
r_symmetry_nbd_other	0.183
r_nbd_refined	0.175
r_nbtor_refined	0.168
r_symmetry_nbd_refined	0.142
r_xyhbond_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.139
r_ncsr_local_group_1	0.109
r_symmetry_xyhbond_nbd_other	0.103
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2017
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	47

Software

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