8BWG | pdb_00008bwg

HRas (1-166) Y64 phosphorylation

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, SITTING DROP		293	Using a commercial crystal screen (HAMPTON RESEARCH, HR2-130) yielded a hit for monophosphorylated HRas under sitting drop conditions (drop size 600 nL) with a 1:1 ratio of protein solution (phospho-HRas 0.4 mM, RasGAP 0.4 mM, Na-HEPES 20 mM pH = 8.0, MgCl2 5 mM, NaF 20 mM) and precipitant (Na-citrate 100 mM pH = 5.6, Li2SO4 1.0 M, CaCl2 200 mM). After three rounds of microseeding well-formed single crystals were obtained using 2.0 uL sitting drops and a 1:1 ratio of protein buffer (HRas 400 uM, RasGAP 400 uM, MgCl2 5 mM, Na-HEPES 20 mM pH = 8.0, NaF 20 mM) and precipitant (Na-Citrate 100 mM pH = 5.6, Li2SO4 800 mM, CaCl2 200 mM). These were harvested using cryoprotectant (80% precipitant, 20% glycerol (v/v)) and sent for data collection.

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.662	α = 90
b = 92.662	β = 90
c = 119.323	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 XE 16M		2021-01-29	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)	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	1.32	47.925	99.2	0.041	0.043	0.014	1	28.6	17.6		45988

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	1.32	1.34			1.34	1.535	0.723	0.577		7.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.32	47.925	45983	2232	99.176	0.137	0.1354	0.14	0.1739	0.17	22.946

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]
-0.796	-0.398		-0.796		2.583

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.648
r_rigid_bond_restr	15.682
r_dihedral_angle_3_deg	14.448
r_dihedral_angle_2_deg	8.675
r_scbond_other	7.62
r_scbond_it	7.604
r_scangle_it	7.202
r_scangle_other	7.192
r_dihedral_angle_1_deg	6.465
r_lrange_it	5.369
r_lrange_other	5.079
r_mcangle_it	3.612
r_mcangle_other	3.61
r_mcbond_it	3.283
r_mcbond_other	3.171
r_angle_refined_deg	1.607
r_angle_other_deg	0.592
r_nbd_refined	0.266
r_xyhbond_nbd_refined	0.222
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.174
r_symmetry_nbd_refined	0.163
r_nbd_other	0.147
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1280
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	34

Software

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