4LHW | pdb_00004lhw

Crystal structure of Rab8 in its active GppNHp-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	6.8	293	Rab8a6-176:GppNHp (15 mg/ml; buffer: 25 mM HEPES, 40 mM NaCl, 1 mM MgCl2, 10 M GppNHp and 5 mM -mercaptoethanol) crystals were produced in 15% (w/v) PEG8000, 7.5 %(v/v) MPD, 0.1 M HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.381	α = 90
b = 96.676	β = 90
c = 105.09	γ = 90

Symmetry
Space Group	P 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	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		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	1.55	19.9	99.2				132605		21.62

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	1.55	19.89	125855	6688	99.2	0.146	0.144	0.16	0.183	0.19	RANDOM	17.43

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]
0.74			-0.73		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.27
r_dihedral_angle_4_deg	18.573
r_dihedral_angle_3_deg	15.317
r_dihedral_angle_1_deg	6.099
r_scangle_it	4.736
r_angle_other_deg	4.147
r_scbond_it	3.178
r_mcangle_it	2.477
r_mcbond_other	2.077
r_mcbond_it	1.482
r_angle_refined_deg	1.479
r_chiral_restr	0.334
r_symmetry_vdw_other	0.299
r_symmetry_vdw_refined	0.255
r_nbd_other	0.249
r_nbd_refined	0.233
r_symmetry_hbond_refined	0.201
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.182
r_nbtor_other	0.11
r_metal_ion_refined	0.024
r_bond_refined_d	0.013
r_gen_planes_other	0.007
r_gen_planes_refined	0.005
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6913
Nucleic Acid Atoms
Solvent Atoms	1049
Heterogen Atoms	173

Software

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