8BOS

Transition state analogue complex of small G protein and its GAP effector

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WQ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	precipitant: HEPES-Na 100 mM pH = 8.0, PEG3350 22% (w/v), (NH4)2SO4 20 mM, Gd-HCl 100 mM, NaF 20 mM protein buffer: HRas 0.400 mM, RasGAP 0.400 mM, HEPES-Na 20 mM, NaF 20 mM drop size: 5 uL, protein:precipitant ratio: 1:1.2

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.832	α = 90
b = 41.558	β = 109.25
c = 89.674	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	PIXEL	DECTRIS EIGER2 XE 16M		2021-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.976	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.1	84.66	54.1	0.176	0.213	0.112	0.981	12.6	3.4		16248

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			0.659	0.821	0.478	0.552	1.7	2.8

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	1WQ1	2.1	84.66	15452	791	54.81	0.20217	0.19802	0.27994	RANDOM	43.913

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]
-0.28		0.04	0.02		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.398
r_long_range_B_refined	7.971
r_long_range_B_other	7.971
r_dihedral_angle_1_deg	7.299
r_dihedral_angle_2_deg	5.693
r_scangle_other	5.381
r_mcangle_other	4.94
r_mcangle_it	4.939
r_scbond_it	3.516
r_scbond_other	3.513
r_mcbond_it	3.218
r_mcbond_other	3.205
r_angle_refined_deg	1.437
r_angle_other_deg	0.46
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3914
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
Aimless	data scaling
MOLREP	phasing
xia2	data reduction