8AOQ | pdb_00008aoq

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a

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, SITTING DROP		294	0.4M Ammonium Phosphate

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.66	α = 90
b = 59.169	β = 90
c = 88.334	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	2.088	49.2	100	0.064	0.999	17.04	7		18215

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	2.09	2.21	99.9		0.857	0.784	2	6.96

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	2.088	49.16	18215	905	99.929	0.196	0.1945	0.2	0.2325	0.24	49.942

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]
0.767			0.492		-1.259

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.906
r_dihedral_angle_3_deg	12.829
r_dihedral_angle_4_deg	10.232
r_dihedral_angle_1_deg	7.181
r_lrange_it	4.333
r_lrange_other	4.332
r_scangle_it	3.116
r_scangle_other	3.115
r_mcangle_it	2.388
r_mcangle_other	2.387
r_scbond_it	1.95
r_scbond_other	1.949
r_mcbond_other	1.539
r_mcbond_it	1.538
r_angle_refined_deg	1.463
r_angle_other_deg	1.263
r_nbd_other	0.211
r_symmetry_nbd_other	0.189
r_nbd_refined	0.172
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.166
r_xyhbond_nbd_refined	0.135
r_symmetry_nbd_refined	0.131
r_ncsr_local_group_1	0.11
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.06
r_bond_refined_d	0.007
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	1885
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	39

Software

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