3GFT | pdb_00003gft

Human K-Ras (Q61H) in complex with a GTP analogue

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AGP	PDB entry 1AGP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.5	291	20% PEG 3350, 0.2M Lithium citrate, pH 4.5, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.535	α = 90
b = 118.275	β = 90
c = 156.836	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	IMAGE PLATE	RIGAKU RAXIS		2007-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	20	99.8	0.151	6.7	6.5		69383

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.17	99.4		0.945		6.2	6812

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 1AGP	2.27	20	55104	2589	99.583	0.215	0.213	0.21	0.267	0.26	Thin resolution shells	23.166

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]
-0.928			1.459		-0.531

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.228
r_dihedral_angle_4_deg	17.393
r_dihedral_angle_3_deg	15.173
r_dihedral_angle_1_deg	5.373
r_scangle_it	3.392
r_mcangle_it	3.197
r_scbond_it	2.219
r_mcbond_it	1.993
r_angle_other_deg	1.823
r_angle_refined_deg	1.423

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.228
r_dihedral_angle_4_deg	17.393
r_dihedral_angle_3_deg	15.173
r_dihedral_angle_1_deg	5.373
r_scangle_it	3.392
r_mcangle_it	3.197
r_scbond_it	2.219
r_mcbond_it	1.993
r_angle_other_deg	1.823
r_angle_refined_deg	1.423
r_mcbond_other	0.483
r_chiral_restr	0.064
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7566
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	212

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.