8CNN | pdb_00008cnn

BeF3 Phospho-HRas GSA complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	Protein buffer (phospho-HRas pY64 0.4 mM, RasGAP 0.4 mM, Na-HEPES 20 mM pH = 8.0, MgCl2 5 mM, NaF 20 mM) was mixed with precipitant in a 1:1 ratio with a total drop size of 600 nL. The precipitant solution consits of: 100 mM NaOAc, pH = 4.5, 200 mM Li2SO4, 50% PEG400 (v/v). Protein crystals were soaked in precipitant solutions containing 50-100 mM BeCl2 and subsequently flash-frozen using 20% glycerol as cryoprotectant.

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.77	α = 90
b = 87.77	β = 90
c = 132.381	γ = 120

Symmetry
Space Group	H 3 2

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 S 16M		2023-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	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	1.48	49.92	100	1	15.8	20.3		32936

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	1.48	1.51	100		0.559	1.2	20.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.48	44.17	31254	1679	99.99	0.16509	0.16384	0.17	0.18838	0.19	RANDOM	22.508

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]
-0.15	-0.07		-0.15		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	13.174
r_dihedral_angle_3_deg	12.621
r_long_range_B_refined	7.393
r_long_range_B_other	7.213
r_scangle_other	5.945
r_dihedral_angle_1_deg	5.798
r_scbond_it	4.076
r_scbond_other	3.99
r_mcangle_other	2.826
r_mcangle_it	2.82
r_mcbond_it	2.08
r_mcbond_other	2.009
r_angle_refined_deg	1.816
r_angle_other_deg	0.923
r_chiral_restr	0.222
r_bond_refined_d	0.015
r_gen_planes_other	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.002
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	1385
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	16

Software

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