9GH2 | pdb_00009gh2

Human KRas4A (GMPPNP) in complex with compound 36

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		unreleased crystal structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	24% PEG 3350, 150 mM MgCl2, 10 mM CoCl2, 100 mM HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.467	α = 90
b = 34.281	β = 109.29
c = 69.591	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS3 6M		2021-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	1.00	Diamond	I24

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	29.5	97.6	0.047	0.057	0.031	0.997	10.3	3		34806

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	1.39	78.6		0.469	0.587	0.349	0.891		2.4

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	1.35	29.5	33076	1729	97.48	0.1838	0.1821	0.193	0.2169	0.2276	RANDOM	30.23

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]
2.85		0.36	0.82		-3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.953
r_dihedral_angle_3_deg	13.933
r_dihedral_angle_4_deg	10.887
r_dihedral_angle_1_deg	3.795
r_rigid_bond_restr	3.515
r_mcangle_it	2.352
r_angle_other_deg	2.31
r_mcbond_it	1.985
r_mcbond_other	1.976
r_angle_refined_deg	1.703

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.953
r_dihedral_angle_3_deg	13.933
r_dihedral_angle_4_deg	10.887
r_dihedral_angle_1_deg	3.795
r_rigid_bond_restr	3.515
r_mcangle_it	2.352
r_angle_other_deg	2.31
r_mcbond_it	1.985
r_mcbond_other	1.976
r_angle_refined_deg	1.703
r_chiral_restr	0.115
r_bond_other_d	0.034
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_gen_planes_other	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1253
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.