5AMH

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, trigonal crystal form

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, 2.2 M CALCIUM CHLORIDE

Crystal Properties
Matthews coefficient	Solvent content
2.3	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.72	α = 90
b = 51.72	β = 90
c = 84.71	γ = 120

Symmetry
Space Group	P 32 2 1

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		2011-06-24	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	1.2	30.8	99.7	0.06	11.85	3.91		41611		-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	1.2	1.27	99.3		0.74	1.78	3.69

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	1.2	30.77	39531	2076	99.82	0.12716	0.12565	0.15737	RANDOM	24.966

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]
0.29	0.15		0.29		-0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.583
r_sphericity_free	30.891
r_sphericity_bonded	19.896
r_dihedral_angle_4_deg	14.455
r_dihedral_angle_3_deg	12.964
r_scbond_it	7.159
r_dihedral_angle_1_deg	6.723
r_rigid_bond_restr	6.304
r_mcangle_it	4.943
r_mcbond_it	4.802
r_mcbond_other	4.774
r_angle_refined_deg	2.398
r_angle_other_deg	1.96
r_chiral_restr	0.127
r_bond_refined_d	0.023
r_gen_planes_refined	0.014
r_gen_planes_other	0.01
r_bond_other_d	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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	827
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	29

Software

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