1YZU

GppNHp-Bound Rab21 GTPase at 2.50 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	6.5	277	15% PEG 4000, 10% Glycerol, 200mM Na thiocyanate, 50mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.87	56.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.834	α = 90
b = 99.719	β = 90
c = 105.76	γ = 90

Symmetry
Space Group	I 21 21 21

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	2003-09-16	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	2.5	50	95.6	0.067	21.2	5		13852			55.7

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)
	2.5	2.57	99.2		0.387	4.8	5	1169

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	2.5	16	13857	13121	679	95.4	0.25	0.21744	0.21354	0.29285	RANDOM	41.242

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]
-3.36			6.5		-3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.517
r_dihedral_angle_4_deg	22.495
r_dihedral_angle_3_deg	15.936
r_dihedral_angle_1_deg	6.42
r_scangle_it	1.908
r_angle_refined_deg	1.42
r_scbond_it	1.321
r_mcangle_it	1.004
r_mcbond_it	0.823
r_angle_other_deg	0.811
r_symmetry_hbond_refined	0.259
r_nbd_refined	0.245
r_symmetry_vdw_other	0.241
r_symmetry_vdw_refined	0.23
r_xyhbond_nbd_refined	0.204
r_nbd_other	0.195
r_nbtor_refined	0.183
r_metal_ion_refined	0.155
r_mcbond_other	0.105
r_nbtor_other	0.084
r_chiral_restr	0.076
r_xyhbond_nbd_other	0.013
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
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	2490
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	66

Software

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