Experiment: 7XKJ

ELECTRON CRYSTALLOGRAPHY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7RPZ

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.88	α = 90
b = 49.28	β = 90
c = 87.2	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

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1

Data Collection

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY		FREE R-VALUE	3	35.51	1.35	6411	651	99.18	0.3134	0.31	0.3243	0.3366	0.3489	30.68

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.3004
f_angle_d	1.6433
f_chiral_restr	0.0915
f_bond_d	0.0108
f_plane_restr	0.0079

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1327
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	73

Software

Software
Software Name	Purpose
PHENIX	refinement

Sample
Isoform 2B of GTPase KRas GUANOSINE-5'-DIPHOSPHATE 4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6-fluoronaphthalen-2-ol MAGNESIUM ION

Specimen Preparation
Sample Aggregation State	3D ARRAY
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	39.868
Length b	51.757
Length c	51.757
Angle Alpha	90
Angle Beta	90
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1 (7RPZ)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	Correlation coefficient
Overall B Value	200
Fitting Procedure
Details	no

Data Acquisition
Detector Type	DIRECT ELECTRON DE-20 (5k x 3k)
Electron Dose (electrons/Å**2)	0.02

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL 2100F
Minimum Defocus (nm)	1500
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DIFFRACTION
Specimen Holder Model	FISCHIONE 2550
Nominal Magnification	6000
Calibrated Magnification	6000
Source	LAB6
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	Coot	0.9.4
MODEL REFINEMENT	PHENIX	1.19.2
MOLECULAR REPLACEMENT	PHENIX	1.19.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE

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.