9Y76 | pdb_00009y76

Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	20% PEG3350, 0.2 M magnesium formate

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.954	α = 90
b = 88.41	β = 97.86
c = 73.556	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 PILATUS3 S 6M		2023-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.18061	CLSI	08B1-1

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	1.56	50	98.1	0.043	0.048	0.02	1	11.2	5.2		86595

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	1.56	1.59	82		0.585	0.675	0.329	0.566		3.7

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	1.56	38.83	82353	4204	98.02	0.16863	0.16659	0.1908	0.20798	0.2219	RANDOM	25.77

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]
-3.49		-1.69	4.37		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	17.253
r_long_range_B_other	16.541
r_dihedral_angle_3_deg	12.226
r_scangle_other	11.008
r_mcangle_other	10.938
r_mcangle_it	10.937
r_rigid_bond_restr	8.484
r_dihedral_angle_1_deg	8.007
r_dihedral_angle_2_deg	7.991
r_scbond_it	7.804
r_scbond_other	7.802
r_mcbond_it	7.783
r_mcbond_other	7.782
r_angle_refined_deg	1.363
r_angle_other_deg	0.488
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4639
Nucleic Acid Atoms
Solvent Atoms	423
Heterogen Atoms	85

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
REFMAC	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction