8OG9 | pdb_00008og9

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 4

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	6.5	293	0.1M MES pH6.5, 2.13M Lithium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.981	α = 90
b = 82.981	β = 90
c = 237.602	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		2015-08-21	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	2.94	53.277	99.6	0.994	7.2	18.5		11003

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	2.94	3.12			0.654

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	2.945	53.277	10938	508	99.654	0.193	0.1905	0.19	0.2404	0.24	57.668

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]
1.019	0.51		1.019		-3.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.318
r_dihedral_angle_4_deg	21.603
r_dihedral_angle_3_deg	17.923
r_dihedral_angle_1_deg	7.868
r_lrange_it	5.094
r_lrange_other	5.061
r_scangle_it	3.181
r_scangle_other	3.127
r_mcangle_it	2.942
r_mcangle_other	2.941
r_scbond_it	1.863
r_scbond_other	1.82
r_mcbond_other	1.695
r_mcbond_it	1.694
r_angle_refined_deg	1.48
r_angle_other_deg	1.184
r_symmetry_nbd_other	0.179
r_nbd_refined	0.176
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.138
r_nbd_other	0.114
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.057
r_symmetry_nbd_refined	0.051
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2387
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	46

Software

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