3LLU

Crystal structure of the nucleotide-binding domain of Ras-related GTP-binding protein C

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	2.0M ammonium sulfate, 0.2M sodium chloride, 0.1M HEPES. 1:100 (w/w) papain and GMPPNP were also added. Please note: mass spectral analysis of TEV protease digest prior to crystallization suggested that removal of the His-tag was incomplete even after 2 days. However, without TEV protease treatment no crystals were obtained using otherwise identical crystallization conditions. Also note the presence of papain in the crystallization drop., pH 7.5, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.22	α = 90
b = 72.22	β = 90
c = 72.182	γ = 90

Symmetry
Space Group	I 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC Q315		2009-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934	APS	19-ID

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	1.4	25	100	0.055	12.5	7.3		36466

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)
	1.4	1.42	100		0.816		7.2	1835

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2Q3F	1.4	22.84	36436	1811	99.956	0.155	0.154	0.181	RANDOM	14.63

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]
-0.282			-0.282		0.563

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.24
r_dihedral_angle_3_deg	11.149
r_dihedral_angle_4_deg	7.143
r_dihedral_angle_1_deg	5.517
r_scangle_it	4.536
r_scbond_it	3.197
r_mcangle_it	1.918
r_angle_refined_deg	1.515
r_mcbond_it	1.263
r_rigid_bond_restr	1.169

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.24
r_dihedral_angle_3_deg	11.149
r_dihedral_angle_4_deg	7.143
r_dihedral_angle_1_deg	5.517
r_scangle_it	4.536
r_scbond_it	3.197
r_mcangle_it	1.918
r_angle_refined_deg	1.515
r_mcbond_it	1.263
r_rigid_bond_restr	1.169
r_angle_other_deg	0.941
r_mcbond_other	0.407
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1516
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	42

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling

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 R01GM133198.