9GGT | pdb_00009ggt

Human KRas4A (GDP) in complex with compound 8

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	6.2	292	25% PEG 8000, 300 mM LiCl, 100 mM bis-tris propane

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.34	α = 90
b = 40.87	β = 90
c = 112.06	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 PILATUS 2M		2014-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9163	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.71	37.34	99.5	0.114	0.141	0.057	12.6	6.1		19159			9.206

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.71	1.75	99.8		0.727	0.902	0.358	2.4	6.1

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	1.71	35.45	18180	931	99.32	0.2099	0.2073	0.2173	0.2628	0.2755	RANDOM	19.072

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]
-1.01			-0.68		1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.352
r_dihedral_angle_4_deg	19.284
r_dihedral_angle_3_deg	15.217
r_dihedral_angle_1_deg	5.147
r_angle_other_deg	2.385
r_angle_refined_deg	2.005
r_mcangle_it	1.513
r_mcbond_it	0.926
r_mcbond_other	0.926
r_chiral_restr	0.128

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.352
r_dihedral_angle_4_deg	19.284
r_dihedral_angle_3_deg	15.217
r_dihedral_angle_1_deg	5.147
r_angle_other_deg	2.385
r_angle_refined_deg	2.005
r_mcangle_it	1.513
r_mcbond_it	0.926
r_mcbond_other	0.926
r_chiral_restr	0.128
r_bond_other_d	0.035
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1368
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	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.