4K81

Crystal structure of the Grb14 RA and PH domains in complex with GTP-loaded H-Ras

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HK0	PDB ENTRIES 3HK0 (CHAINS A,C,E,G) AND 1LFD (CHAINS B,D,F,H)
experimental model	PDB	1LFD	PDB ENTRIES 3HK0 (CHAINS A,C,E,G) AND 1LFD (CHAINS B,D,F,H)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	315	14% (w/v) PEG 3350, 100 mM MES, pH 5.9, 200 mM MgCl2, 2% glycerol, and 3% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 315K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.727	α = 90
b = 115.593	β = 96.75
c = 103.107	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 315		2011-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.000	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.4	50	99.9	0.058	23.8	3.7		71989

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 3HK0 (CHAINS A,C,E,G) AND 1LFD (CHAINS B,D,F,H)	2.4	50	68338	3628	99.65	0.22149	0.21853	0.2769	RANDOM	66.457

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]
1.97		0.8	0.69		-2.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.702
r_dihedral_angle_4_deg	17.731
r_dihedral_angle_3_deg	16.15
r_dihedral_angle_1_deg	6.046
r_angle_refined_deg	1.233
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13500
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	186

Software

Software
Software Name	Purpose
REFMAC	refinement