1S8F | pdb_00001s8f

Crystal structure of Rab9 complexed to GDP reveals a dimer with an active conformation of switch II

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KY3	PDB entry 1ky3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	PEG8000, Na-benzoate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.17	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.245	α = 90
b = 98.245	β = 90
c = 79.66	γ = 90

Symmetry
Space Group	I 41

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		2003-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	1.0091	EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.77	30	99.9	0.053	24.8	3.8		37662			22.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.77	1.83	99.9		0.0691	2.5	3.8	3752

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	PDB entry 1ky3	1.77	30	35770	35770	1825	99.9	0.1646	0.16	0.2213	0.21	keep twin-related reflection in same set	30

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
4	2550	3027.5

RMS Deviations
Key	Refinement Restraint Deviation
s_similar_adp_cmpnt	0.08
s_non_zero_chiral_vol	0.039
s_zero_chiral_vol	0.033
s_from_restr_planes	0.0255
s_angle_d	0.023
s_anti_bump_dis_restr	0.017
s_bond_d	0.007
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2712
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	96

Software

Software
Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
COMO	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 R01GM157729.