9G4B | pdb_00009g4b

Human KRas4A (GDP) in complex with compound 15

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	8.7	292	25% PEG 8000, 500 mM LiCl, 100 mM bis-tris propane

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.01	α = 90
b = 40.14	β = 90
c = 110.66	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 PILATUS3 6M		2016-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97632	Diamond	I03

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	1.14	37.01	100	0.047	0.052	0.021	18.2	5.9		61058			10.387

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.14	1.16	97.8		0.9	0.479	1.6	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	1.14	35.12	57986	2993	99.83	0.1648	0.1634	0.1717	0.1926	0.1975	RANDOM	15.899

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]
0.33			-0.32		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.972
r_dihedral_angle_4_deg	16.363
r_dihedral_angle_3_deg	12.77
r_dihedral_angle_1_deg	5.066
r_angle_other_deg	2.354
r_rigid_bond_restr	2.227
r_angle_refined_deg	2.094
r_mcangle_it	1.903
r_mcbond_it	1.54
r_mcbond_other	1.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.972
r_dihedral_angle_4_deg	16.363
r_dihedral_angle_3_deg	12.77
r_dihedral_angle_1_deg	5.066
r_angle_other_deg	2.354
r_rigid_bond_restr	2.227
r_angle_refined_deg	2.094
r_mcangle_it	1.903
r_mcbond_it	1.54
r_mcbond_other	1.54
r_chiral_restr	0.132
r_bond_other_d	0.035
r_bond_refined_d	0.017
r_gen_planes_other	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1362
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	77

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.