8OG6 | pdb_00008og6

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 1

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	293	0.1M Tris pH 7.0, 2.13M Lithium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.228	α = 90
b = 82.228	β = 90
c = 237.782	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 PILATUS 6M		2015-03-06	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	52.76	100	0.999	17.2	12.6		24916

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			0.717

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	2.245	45.677	23687	1139	99.97	0.204	0.2027	0.21	0.2308	0.23	47.665

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]
0.635	0.317		0.635		-2.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.673
r_dihedral_angle_4_deg	17.654
r_dihedral_angle_3_deg	16.403
r_dihedral_angle_1_deg	9.366
r_lrange_it	8.188
r_lrange_other	8.114
r_scangle_it	4.462
r_scangle_other	4.46
r_mcangle_it	3.917
r_mcangle_other	3.917
r_scbond_it	2.846
r_scbond_other	2.844
r_mcbond_it	2.561
r_mcbond_other	2.554
r_angle_refined_deg	2.15
r_angle_other_deg	1.427
r_nbd_refined	0.215
r_nbd_other	0.199
r_xyhbond_nbd_refined	0.192
r_symmetry_nbd_other	0.189
r_symmetry_nbd_refined	0.189
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.142
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.02
r_gen_planes_refined	0.013
r_gen_planes_other	0.009
r_bond_other_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2385
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	44

Software

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