8OGA | pdb_00008oga

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PXW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1M Tris pH 7.5, 1.66M Lithium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.581	α = 90
b = 81.581	β = 90
c = 234.805	γ = 120

Symmetry
Space Group	P 61 2 2

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 S 16M		2022-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	46.96	100	0.995	16	29.5		24491

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27			0.703

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.2	45.191	24406	1237	99.984	0.187	0.1853	0.19	0.2086	0.21	59.031

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]
0.24	0.12		0.24		-0.779

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.512
r_dihedral_angle_4_deg	24.574
r_dihedral_angle_3_deg	17.288
r_dihedral_angle_1_deg	8.565
r_lrange_it	8.344
r_lrange_other	8.215
r_scangle_it	6.135
r_scangle_other	5.943
r_mcangle_other	4.695
r_mcangle_it	4.691
r_scbond_it	4.26
r_scbond_other	4.068
r_mcbond_it	3.095
r_mcbond_other	3.085
r_angle_refined_deg	1.988
r_angle_other_deg	1.437
r_nbd_other	0.231
r_symmetry_nbd_other	0.198
r_nbd_refined	0.197
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.12
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2363
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing