3CPI

Crystal structure of yeast Rab-GDI

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.46	α = 90
b = 159.78	β = 90.25
c = 77.093	γ = 90

Symmetry
Space Group	P 1 21 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 325 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9795	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	2.3	19.97	98.5			60538	59630	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.35	80

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	PDB ENTRY 1ukv, chain G	2.3	19.97	60538	56646	2982	100	0.2	0.1992	0.19688	0.2426	RANDOM	38.073

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]
-0.48		-0.07	-0.41		0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.562
r_dihedral_angle_4_deg	15.921
r_dihedral_angle_3_deg	15.863
r_dihedral_angle_1_deg	5.419
r_scangle_it	1.866
r_scbond_it	1.136
r_angle_refined_deg	1.058
r_mcangle_it	0.954
r_mcbond_it	0.533
r_nbtor_refined	0.302
r_nbd_refined	0.187
r_symmetry_hbond_refined	0.143
r_xyhbond_nbd_refined	0.134
r_symmetry_vdw_refined	0.113
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6979
Nucleic Acid Atoms
Solvent Atoms	797
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XDS	data scaling
MOLREP	phasing