8OGB

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 8

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, 2.13M Lithium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.018	α = 90
b = 85.018	β = 90
c = 219.36	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		2016-04-18	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	2.27	219.36	100	0.998	14.8	18.8		22640

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	2.27	2.34			0.784

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.27	61.206	22549	1129	99.951	0.17	0.1682	0.2125	39.147

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]
-0.229	-0.115		-0.229		0.743

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.975
r_dihedral_angle_4_deg	18.091
r_dihedral_angle_3_deg	17.562
r_dihedral_angle_1_deg	8.356
r_lrange_it	7.676
r_lrange_other	7.613
r_scangle_it	5.098
r_scangle_other	5.097
r_mcangle_it	4.115
r_mcangle_other	4.114
r_scbond_it	3.22
r_scbond_other	3.219
r_mcbond_it	2.617
r_mcbond_other	2.6
r_angle_refined_deg	2.049
r_angle_other_deg	1.46
r_symmetry_xyhbond_nbd_refined	0.228
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.195
r_nbd_refined	0.193
r_nbtor_refined	0.182
r_symmetry_nbd_refined	0.167
r_nbd_other	0.164
r_symmetry_xyhbond_nbd_other	0.097
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.017
r_xyhbond_nbd_other	0.016
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2384
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	44

Software

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