1YZT

GppNHp-Bound Rab21 GTPase at 2.05 A Resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Polyalanine Rab3a GTPase

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	18% PEG 6000, 200mM Lithium sufate, 50mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.75	54.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.357	α = 90
b = 36.567	β = 113.4
c = 86.666	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	MAR scanner 300 mm plate	Osmic mirror	2004-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	2.05	50	99.8	0.08	15.8	4		23946			35.1

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)
	2.05	2.11	98.1		0.368	3.8	4	1952

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	Polyalanine Rab3a GTPase	2.05	12	24116	22613	1219	99.88	0.232	0.21425	0.21041	0.28586	RANDOM	23.139

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]
-0.84		-0.9	0.66		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.772
r_dihedral_angle_4_deg	19.942
r_dihedral_angle_3_deg	13.691
r_dihedral_angle_1_deg	6.137
r_scangle_it	2.43
r_scbond_it	1.8
r_angle_refined_deg	1.26
r_mcbond_it	1.105
r_mcangle_it	1.028
r_angle_other_deg	0.755
r_xyhbond_nbd_refined	0.211
r_nbd_refined	0.209
r_symmetry_hbond_refined	0.2
r_nbd_other	0.196
r_symmetry_vdw_other	0.18
r_nbtor_refined	0.175
r_symmetry_vdw_refined	0.154
r_mcbond_other	0.105
r_nbtor_other	0.082
r_chiral_restr	0.069
r_xyhbond_nbd_other	0.042
r_metal_ion_refined	0.042
r_bond_refined_d	0.01
r_bond_other_d	0.006
r_gen_planes_refined	0.003
r_gen_planes_other	0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2395
Nucleic Acid Atoms
Solvent Atoms	475
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing