6UZK | pdb_00006uzk

Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HDO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20-25% PEG 3,350, 100 mM Tris, pH 8.5, 100 mM KCl

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.204	α = 90
b = 77.089	β = 91.558
c = 58.41	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315r		2019-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.999995	ALS	5.0.3

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	1.92	50	94	0.991	16.33	3		36147

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	1.92	1.95			0.486

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4hdo	1.924	36.514	36123	1772	93.712	0.223	0.2201	0.2861	48.081

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]
-0.834		2.847	-1.463		2.139

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.315
r_dihedral_angle_4_deg	18.472
r_dihedral_angle_3_deg	18.01
r_dihedral_angle_1_deg	7.056
r_lrange_it	6.197
r_mcangle_it	3.309
r_scangle_it	2.768
r_mcbond_it	1.777
r_scbond_it	1.539
r_angle_refined_deg	1.069
r_nbtor_refined	0.314
r_nbd_refined	0.216
r_symmetry_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.183
r_xyhbond_nbd_refined	0.128
r_metal_ion_refined	0.096
r_chiral_restr	0.084
r_gen_planes_refined	0.004
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3809
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing