5AMI

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, Wash I structure

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				100 MM SODIUM ACETATE PH 4.6, 20 %(W/V) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
1.8	30

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.25	α = 90
b = 59.656	β = 90
c = 86.728	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 PILATUS 6M		2013-12-13	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.75	37.3	99.7	0.05	16.98	4.23		30628		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.86	98.7		0.68	1.9	4.23

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4V2Y	1.75	37.29	29087	1540	99.75	0.16727	0.16508	0.20942	RANDOM	36.758

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]
1.1			0.03		-1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.268
r_dihedral_angle_3_deg	13.114
r_dihedral_angle_4_deg	12.405
r_dihedral_angle_1_deg	6.22
r_mcangle_it	2.566
r_scbond_it	2.525
r_angle_refined_deg	2.235
r_mcbond_it	1.665
r_mcbond_other	1.664
r_angle_other_deg	1.155
r_chiral_restr	0.123
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2232
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	41

Software

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