9GGZ | pdb_00009ggz

Human KRas4A (GMPPNP) in complex with compound 31

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, 100 mM MgCl2, 10 mM CoCl2, 100 mM HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.254	α = 90
b = 34.866	β = 108.63
c = 69.575	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 EIGER X 16M		2020-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	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	1.37	28.78	99.4	0.031	0.036	0.02	1	19.4	3.4		34572

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	1.37	1.41	96		0.61	0.729	0.394	0.828		3.3

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	1.37	28.78	32779	1711	99.15	0.1797	0.1771	0.1932	0.2311	0.2473	RANDOM	23.237

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]
-0.37		-0.31	1.76		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.605
r_dihedral_angle_4_deg	17.791
r_dihedral_angle_3_deg	13.601
r_dihedral_angle_1_deg	4.159
r_mcangle_it	3.192
r_rigid_bond_restr	3.127
r_mcbond_it	2.835
r_mcbond_other	2.833
r_angle_other_deg	2.438
r_angle_refined_deg	2.289

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.605
r_dihedral_angle_4_deg	17.791
r_dihedral_angle_3_deg	13.601
r_dihedral_angle_1_deg	4.159
r_mcangle_it	3.192
r_rigid_bond_restr	3.127
r_mcbond_it	2.835
r_mcbond_other	2.833
r_angle_other_deg	2.438
r_angle_refined_deg	2.289
r_chiral_restr	0.131
r_bond_other_d	0.034
r_bond_refined_d	0.022
r_gen_planes_other	0.022
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1301
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	77

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.