6R18 | pdb_00006r18

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 11a

X-RAY DIFFRACTION

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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	0.4 M Ammonium phosphate

Crystal Properties
Matthews coefficient	Solvent content
1.81	32.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.63	α = 90
b = 59.592	β = 90
c = 88.894	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-F		2018-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1	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	1.35	44.45	99.9	0.074	0.999	17.62	12.7		66849

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	1.35	1.43	99.3		0.96	0.83	1.97	12.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4v2y	1.35	44.45	63530	3318	99.88	0.17409	0.17287	0.18	0.19732	0.2	RANDOM	21.506

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]
-0.31			0.52		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.598
r_dihedral_angle_3_deg	12.169
r_dihedral_angle_4_deg	11.36
r_dihedral_angle_1_deg	6.752
r_long_range_B_refined	5.213
r_long_range_B_other	5.209
r_scangle_other	3.18
r_mcangle_it	2.299
r_mcangle_other	2.299
r_angle_refined_deg	2.148
r_scbond_it	2.028
r_scbond_other	2.023
r_mcbond_it	1.41
r_mcbond_other	1.41
r_angle_other_deg	1.066
r_chiral_restr	0.128
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2564
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	77

Software

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