7QJK

Crystal structure of PDE6D in complex with Compound-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TB5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	1.2 M AmSO4 and 0.1 M ammonium acetate pH 4.9 at 291K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.548	α = 90
b = 76.548	β = 90
c = 238.018	γ = 90

Symmetry
Space Group	P 41 21 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 EIGER X 16M		2019-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97951	Diamond	I04

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	3.1	76.55	90.6	0.975	5.6	8		12108

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	3.1	3.31			0.343

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	5TB5	3.1	64.463	12095	625	88.829	0.248	0.2464	0.2831	76.627

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]
-0.979			-0.979		1.958

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.758
r_dihedral_angle_3_deg	19.209
r_dihedral_angle_4_deg	17.759
r_lrange_it	10.666
r_lrange_other	10.665
r_scangle_it	7.244
r_scangle_other	7.242
r_mcangle_it	6.668
r_mcangle_other	6.667
r_dihedral_angle_1_deg	5.988
r_scbond_it	4.284
r_scbond_other	4.282
r_mcbond_it	4.159
r_mcbond_other	4.153
r_chiral_restr_other	2.517
r_angle_other_deg	1.105
r_angle_refined_deg	1.091
r_nbd_other	0.307
r_symmetry_nbd_refined	0.306
r_symmetry_nbd_other	0.221
r_ncsr_local_group_6	0.213
r_ncsr_local_group_5	0.212
r_nbd_refined	0.209
r_ncsr_local_group_3	0.209
r_symmetry_xyhbond_nbd_refined	0.208
r_ncsr_local_group_4	0.182
r_ncsr_local_group_2	0.181
r_ncsr_local_group_1	0.178
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.17
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_other	0.054
r_chiral_restr	0.034
r_bond_refined_d	0.002
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4674
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	79

Software

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