1YZL

GppNHp-Bound Rab9 GTPase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Polyalanine Rab4 GTPase

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	20% PEG 6000, 200mM Magnesium Chloride, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.325	α = 90
b = 68.325	β = 90
c = 83.229	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	IMAGE PLATE	MAR scanner 300 mm plate	osmic mirror	2003-08-21	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	1.85	50	99.2	0.06	26.2	7		19409			32.8

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)
	1.85	1.9			0.394	5	7	19418

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 Rab4 GTPase	1.85	4.8	19418	17308	925	99.62	0.215	0.19327	0.19179	0.22084	RANDOM	21.02

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]
0.12	0.06		0.12		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.622
r_dihedral_angle_4_deg	20.894
r_dihedral_angle_3_deg	11.797
r_dihedral_angle_1_deg	5.804
r_scangle_it	1.914
r_scbond_it	1.344
r_angle_refined_deg	1.158
r_mcangle_it	0.958
r_mcbond_it	0.884
r_angle_other_deg	0.81
r_nbd_refined	0.214
r_nbd_other	0.185
r_symmetry_hbond_refined	0.185
r_nbtor_refined	0.182
r_symmetry_vdw_other	0.16
r_xyhbond_nbd_refined	0.154
r_xyhbond_nbd_other	0.119
r_symmetry_vdw_refined	0.104
r_mcbond_other	0.103
r_nbtor_other	0.079
r_chiral_restr	0.067
r_metal_ion_refined	0.027
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
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	1369
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	33

Software

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