7Q9S | pdb_00007q9s

Crystal structure of PDE6D KRas peptide complex with Compound-1

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		291	0.2 M Lithium sulphate, 0.1M Tris pH 8.5 and 20% PEG 3000

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.104	α = 90
b = 81.123	β = 90
c = 118.514	γ = 90

Symmetry
Space Group	C 2 2 21

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		2018-10-15	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	1.85	40.657	100	0.999	8.4	8.4		32070

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	1.85	1.9			0.88

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	1.85	40.657	32034	1575	99.906	0.201	0.1993	0.2031	0.2273	0.2273	31.262

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]
0.019			-0.226		0.207

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.833
r_dihedral_angle_3_deg	16.996
r_dihedral_angle_4_deg	16.271
r_lrange_it	8.79
r_lrange_other	8.789
r_dihedral_angle_1_deg	6.885
r_scangle_it	6.561
r_scangle_other	6.56
r_scbond_it	4.319
r_scbond_other	4.318
r_mcangle_it	3.825
r_mcangle_other	3.824
r_mcbond_it	2.893
r_mcbond_other	2.892
r_angle_other_deg	1.434
r_angle_refined_deg	1.379
r_nbd_refined	0.498
r_symmetry_xyhbond_nbd_other	0.388
r_xyhbond_nbd_refined	0.306
r_symmetry_nbd_other	0.297
r_nbd_other	0.289
r_symmetry_nbd_refined	0.228
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.122
r_symmetry_nbtor_other	0.095
r_chiral_restr	0.054
r_chiral_restr_other	0.006
r_bond_refined_d	0.004
r_bond_other_d	0.004
r_gen_planes_refined	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2489
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	113

Software

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