9OHQ | pdb_00009ohq

Structure of CRBN:IKZF2:Compound 15

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	0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.04	α = 90
b = 70.13	β = 90
c = 78.74	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 9M		2022-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.9001	NSLS-II	17-ID-1

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	1.6	20.1	97.47	0.147	0.998	11.6	12.7		61174

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	1.6	1.63			0.987	0.814		8.3

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	1.6	20.1	61174	3273	97.47	0.17351	0.17195	0.1813	0.20148	0.2072	RANDOM	17.234

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]
0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.129
r_dihedral_angle_2_deg	10.175
r_dihedral_angle_1_deg	6.636
r_long_range_B_refined	5.853
r_long_range_B_other	5.755
r_scangle_other	4.482
r_scbond_it	2.864
r_scbond_other	2.863
r_mcangle_it	2.855
r_mcangle_other	2.855
r_mcbond_it	1.946
r_mcbond_other	1.915
r_angle_refined_deg	1.682
r_angle_other_deg	0.588
r_chiral_restr	0.086
r_gen_planes_refined	0.01
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4286
Nucleic Acid Atoms
Solvent Atoms	439
Heterogen Atoms	144

Software

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