7Q9R | pdb_00007q9r

Cocrystal structure of PDE6D bound to NRAS peptide

X-RAY DIFFRACTION

---

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		279	0.1 M citric acid pH 4.0 and 3.2 M AmSO4

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.788	α = 90
b = 55.788	β = 90
c = 114.842	γ = 120

Symmetry
Space Group	P 32 2 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 EIGER X 16M		2019-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	2.5	114.87	100	0.995	10.5	9.5		7634

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	2.5	2.56			0.859

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5TB5	2.5	48.36	7602	346	99.974	0.235	0.2335	0.24	0.2759	0.27	28.585

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]
0.731	0.366		0.731		-2.373

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.145
r_dihedral_angle_4_deg	17.789
r_dihedral_angle_3_deg	15.165
r_dihedral_angle_1_deg	6.695
r_lrange_it	2.696
r_lrange_other	2.687
r_mcangle_it	1.169
r_mcangle_other	1.168
r_angle_refined_deg	1.016
r_angle_other_deg	0.997
r_scangle_it	0.668
r_scangle_other	0.668
r_mcbond_it	0.618
r_mcbond_other	0.618
r_scbond_it	0.327
r_scbond_other	0.325
r_nbd_other	0.285
r_symmetry_nbd_other	0.223
r_symmetry_nbd_refined	0.202
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.096
r_symmetry_xyhbond_nbd_other	0.081
r_symmetry_nbtor_other	0.07
r_chiral_restr	0.019
r_gen_planes_refined	0.002
r_bond_refined_d	0.001
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1197
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing