8UJY | pdb_00008ujy

Crystal structure of human WD repeat-containing protein 5 in complex with 4-(3,5-dimethoxybenzyl)-9-(4-fluoro-2-methylphenyl)-7-((2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl)methyl)-3,4-dihydrobenzo[f][1,4]oxazepin-5(2H)-one (compound 8)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EG6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	0.1 M Bis-Tris pH 7.0, 0.2 M ammonium acetate, 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.81	α = 88.04
b = 47.68	β = 89.27
c = 68.869	γ = 74.66

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-300		2018-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.01	28.658	90.4	0.079	0.112	0.079	0.996	7	3.9		34546

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.01	2.06	95.7		0.321	0.46	0.321	0.885	2.6	3.8

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	2.01	28.658	34545	1714	90.387	0.191	0.1884	0.2	0.2322	0.24	22.378

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]
-0.913	-0.302	0.306	2.28	-0.024	-1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.079
r_dihedral_angle_other_2_deg	16.927
r_dihedral_angle_6_deg	14.223
r_dihedral_angle_3_deg	12.805
r_dihedral_angle_1_deg	8.222
r_lrange_it	7.028
r_lrange_other	6.845
r_scangle_it	3.872
r_scangle_other	3.871
r_mcangle_it	3.79
r_mcangle_other	3.79
r_scbond_it	2.51
r_scbond_other	2.51
r_mcbond_it	2.473
r_mcbond_other	2.473
r_angle_refined_deg	1.532
r_angle_other_deg	0.526
r_symmetry_xyhbond_nbd_refined	0.25
r_xyhbond_nbd_refined	0.237
r_symmetry_nbd_refined	0.232
r_nbd_other	0.212
r_symmetry_nbd_other	0.202
r_nbd_refined	0.19
r_nbtor_refined	0.177
r_ncsr_local_group_1	0.089
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.057
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4658
Nucleic Acid Atoms
Solvent Atoms	480
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing