8CNJ | pdb_00008cnj

HRas(1-166) in complex with GDP and BeF3-

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	BeF3- GSA complexes were obtained under vapour diffusion sitting drop conditions. Protein buffer (HRas pY64 or HRas 0.4 mM, Na-HEPES 20 mM pH = 8.0, MgCl2 5 mM, NaF 20 mM) were mixed with precipitant in a 1:1 ratio with a total drop size of 600 nL. The precipitant solution consited of: (30 % (v/v) MPD, 100 mM imidazole, pH = 7.0). Protein crystals were soaked in their respective precipitant solutions containing 50 mM BeCl2 and subsequently flash-frozen using 20% glycerol as cryoprotectant.

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.433	α = 90
b = 51.957	β = 90
c = 136.149	γ = 90

Symmetry
Space Group	P 21 21 21

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 X 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)	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	1.35	51.96	96.2	0.093	0.1	0.038	0.999	13.7	12.6		69077

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	1.35	1.37			1.532	1.712	0.743	0.598		8.6

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.35	48.589	68993	3548	96.222	0.145	0.1432	0.14	0.1791	0.18	RANDOM	18.638

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]
1.751			0.154		-1.905

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.511
r_dihedral_angle_3_deg	12.421
r_dihedral_angle_2_deg	8.076
r_dihedral_angle_1_deg	6.23
r_rigid_bond_restr	2.674
r_lrange_it	2.526
r_lrange_other	2.196
r_scangle_it	1.417
r_scangle_other	1.417
r_angle_refined_deg	1.412
r_mcangle_it	1.267
r_mcangle_other	1.267
r_scbond_other	0.998
r_scbond_it	0.997
r_mcbond_it	0.84
r_mcbond_other	0.839
r_angle_other_deg	0.47
r_nbd_refined	0.225
r_chiral_restr	0.219
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.178
r_nbd_other	0.154
r_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_refined	0.13
r_symmetry_nbd_refined	0.123
r_symmetry_nbtor_other	0.076
r_dihedral_angle_other_2_deg	0.06
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2644
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	74

Software

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