4LHV | pdb_00004lhv

Crystal structure of Rab8 in its inactive GDP-bound form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YZQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.836	α = 90
b = 75.95	β = 98.44
c = 106.618	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	CCD	MARMOSAIC 225 mm CCD		2009-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9786	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	20	99.2			67917	67378	3.8	19.16

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (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	THROUGHOUT	1YZQ	1.95	19.96	63957	3388	99.28	0.20441	0.20229	0.21	0.24428	0.25	RANDOM	36.651

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]
1.04		-0.2	0.56		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.63
r_dihedral_angle_4_deg	16.237
r_dihedral_angle_3_deg	15.796
r_dihedral_angle_1_deg	6.146
r_mcbond_other	4.325
r_angle_other_deg	4.199
r_scangle_it	3.299
r_mcangle_it	2.964
r_scbond_it	2.08
r_mcbond_it	1.904
r_angle_refined_deg	1.354
r_symmetry_vdw_refined	0.308
r_symmetry_hbond_refined	0.26
r_nbd_other	0.241
r_symmetry_vdw_other	0.24
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.183
r_nbtor_other	0.112
r_metal_ion_refined	0.099
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_gen_planes_other	0.005
r_gen_planes_refined	0.004
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6273
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	145

Software

Software
Software Name	Purpose
MOSFLM	data reduction
PHASES	phasing
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling