9OHR | pdb_00009ohr

Structure of CRBN:IKZF2:Compound 35

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7LPS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.463	α = 99.92
b = 45.27	β = 90.58
c = 65.493	γ = 104.38

Symmetry
Space Group	P 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 EIGER2 XE 16M		2022-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97628	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.34	29.68	94.8	0.182	0.225	0.13	0.908	5.7	3.2		19467

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.34	2.42		97	0.571	0.687	0.377	0.503		3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.34	29.68	18455	992	94.74	0.22768	0.2244	0.2297	0.28975	0.2903	RANDOM	37.426

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]
0.02		-0.01	-0.02	-0.08	0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	10.99
r_long_range_B_refined	8.282
r_long_range_B_other	8.282
r_dihedral_angle_1_deg	7.823
r_mcangle_it	5.584
r_mcangle_other	5.583
r_scangle_other	4.986
r_mcbond_it	3.535
r_mcbond_other	3.534
r_scbond_it	3.199

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	10.99
r_long_range_B_refined	8.282
r_long_range_B_other	8.282
r_dihedral_angle_1_deg	7.823
r_mcangle_it	5.584
r_mcangle_other	5.583
r_scangle_other	4.986
r_mcbond_it	3.535
r_mcbond_other	3.534
r_scbond_it	3.199
r_scbond_other	3.199
r_angle_refined_deg	1.502
r_angle_other_deg	0.544
r_bond_refined_d	0.006
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	4211
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	157

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.