1SVI

Crystal Structure of the GTP-binding protein YsxC complexed with GDP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	PG 4000, isopropanol, N Hepes buffer, GDP,MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.179	α = 90
b = 68.305	β = 94.05
c = 61.999	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARRESEARCH		2002-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	10	94.8				13194	2	2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	THROUGHOUT	1.95	10	12485	641	94.13	0.17831	0.17614	0.22174	RANDOM	17.442

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]
0.34		-0.58	-0.53		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.494
r_dihedral_angle_1_deg	3.397
r_scangle_it	3.031
r_scbond_it	1.791
r_angle_refined_deg	1.287
r_mcangle_it	1.061
r_symmetry_hbond_refined	0.63
r_mcbond_it	0.547
r_nbd_refined	0.235
r_symmetry_vdw_refined	0.231

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.494
r_dihedral_angle_1_deg	3.397
r_scangle_it	3.031
r_scbond_it	1.791
r_angle_refined_deg	1.287
r_mcangle_it	1.061
r_symmetry_hbond_refined	0.63
r_mcbond_it	0.547
r_nbd_refined	0.235
r_symmetry_vdw_refined	0.231
r_xyhbond_nbd_refined	0.214
r_chiral_restr	0.089
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1457
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
MLPHARE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.