7Q9Q

Crystal structure of PDE6D Geranylgeranylated cystein complex

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, SITTING DROP		277	30% w/v PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.048	α = 77.725
b = 35.289	β = 68.98
c = 37.645	γ = 69.228

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	PIXEL	DECTRIS EIGER2 X 16M		2019-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1	NSLS	X6A

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	1.45	34.971	95.9	1	17.98	3.5		24436

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	1.45	1.49			0.669

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	1.45	34.971	24436	1222	96.193	0.228	0.2251	0.2736	29.697

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]
-1.546	0.939	-0.111	0.583	-0.592	1.126

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.333
r_dihedral_angle_3_deg	15.033
r_dihedral_angle_4_deg	8.193
r_dihedral_angle_1_deg	6.659
r_lrange_it	6.14
r_lrange_other	6.117
r_scangle_it	4.751
r_scangle_other	4.749
r_mcangle_it	3.376
r_mcangle_other	3.376
r_scbond_it	3.228
r_scbond_other	3.226
r_mcbond_it	2.478
r_mcbond_other	2.474
r_angle_refined_deg	1.839
r_angle_other_deg	1.663
r_symmetry_xyhbond_nbd_other	0.244
r_symmetry_nbd_other	0.212
r_nbd_refined	0.205
r_nbd_other	0.193
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.131
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.083
r_gen_planes_refined	0.012
r_gen_planes_other	0.009
r_bond_refined_d
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1208
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	40

Software

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