8OGC | pdb_00008ogc

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 11

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, 2.18M Lithium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.74	α = 90
b = 81.74	β = 90
c = 234.101	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		2016-12-12	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	2.09	234.1	100	0.999	14.3	19		28474

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	2.09	2.15			0.746

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	2.09	70.889	28381	1412	100	0.173	0.1713	0.18	0.2015	0.21	34.24

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]
0.215	0.108		0.215		-0.698

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.598
r_dihedral_angle_3_deg	16.265
r_dihedral_angle_4_deg	14.044
r_dihedral_angle_1_deg	8.724
r_lrange_it	7.322
r_lrange_other	7.103
r_scangle_it	4.315
r_scangle_other	4.065
r_mcangle_it	3.245
r_mcangle_other	3.245
r_scbond_it	2.85
r_scbond_other	2.642
r_angle_refined_deg	2.211
r_mcbond_it	2.049
r_mcbond_other	2.039
r_angle_other_deg	1.459
r_chiral_restr	0.291
r_symmetry_nbd_other	0.191
r_nbd_refined	0.187
r_symmetry_nbd_refined	0.187
r_nbtor_refined	0.182
r_nbd_other	0.158
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2384
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	87

Software

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