7Q9U | pdb_00007q9u

Crystal structure of the high affinity KRas mutant PDE6D complex

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		291	0.2 M Ammonium sulphate, 0.1 M tri sodium citrate pH 5.6, 15 % w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.086	α = 82.771
b = 57.925	β = 81.709
c = 78.913	γ = 68.447

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 PILATUS 6M		2017-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97628	Diamond	I03

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	2.238	53.706	94.7	0.995	6.1	1.7		37781

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	2.24	2.3			0.742

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	2.238	53.706	37435	1774	93.496	0.202	0.1994	0.2	0.2545	0.25	46.809

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]
-0.621	-0.994	-0.933	0.469	0.805	-0.876

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.168
r_dihedral_angle_4_deg	18.934
r_dihedral_angle_3_deg	18.179
r_lrange_it	9.087
r_lrange_other	9.086
r_scangle_it	7.043
r_scangle_other	7.042
r_dihedral_angle_1_deg	6.981
r_mcangle_it	5.402
r_mcangle_other	5.401
r_scbond_it	4.566
r_scbond_other	4.566
r_mcbond_it	3.676
r_mcbond_other	3.676
r_angle_refined_deg	1.609
r_angle_other_deg	1.341
r_symmetry_xyhbond_nbd_refined	0.251
r_symmetry_nbd_refined	0.25
r_nbd_other	0.248
r_nbd_refined	0.2
r_symmetry_nbd_other	0.198
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.159
r_ncsr_local_group_1	0.097
r_symmetry_nbtor_other	0.083
r_ncsr_local_group_2	0.076
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.033
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_bond_refined_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5140
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	137

Software

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