1YR7

PAB0955 crystal structure : a GTPase in GTP-gamma-S bound form from Pyrococcus abyssi

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	13% PEG 4000, 0.2M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 20mM DTT, 0.65mM GTP-gamma-S, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2	38.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.17	α = 90
b = 60.17	β = 90
c = 115.89	γ = 120

Symmetry
Space Group	P 32 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	CCD	MARRESEARCH	mirror	2004-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.08	50	94.6	0.069	0.069	17.75	6.5	15141	15034			45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.08	2.15	64.2		0.232	0.232	6.36	4.7	893

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1YR6	2.08	15	13196	12488	1587	83.18	0.21691	0.21691	0.20835	0.29463	RANDOM	45.443

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]
1.8	0.9		1.8		-2.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.069
r_dihedral_angle_3_deg	18.189
r_dihedral_angle_4_deg	17.661
r_dihedral_angle_1_deg	5.595
r_scangle_it	1.921
r_mcangle_it	1.809
r_scbond_it	1.429
r_angle_refined_deg	1.296
r_mcbond_it	1.084
r_symmetry_hbond_refined	0.411

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.069
r_dihedral_angle_3_deg	18.189
r_dihedral_angle_4_deg	17.661
r_dihedral_angle_1_deg	5.595
r_scangle_it	1.921
r_mcangle_it	1.809
r_scbond_it	1.429
r_angle_refined_deg	1.296
r_mcbond_it	1.084
r_symmetry_hbond_refined	0.411
r_symmetry_vdw_refined	0.36
r_nbtor_refined	0.331
r_xyhbond_nbd_refined	0.324
r_nbd_refined	0.261
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1981
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
AMoRE	phasing

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.