3TW8

GEF domain of DENND 1B in complex with Rab GTPase Rab35

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	289	0.1 M Magnesium Formate, 19% PEG 3350, 0.1 M HEPES (pH 7.4), 4mM n-Nonyl-beta-D-glucoside, 289K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.588	α = 90
b = 56.563	β = 95.63
c = 175.305	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	ADSC QUANTUM 315		2011-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	0.9795	NSLS	X25

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	2.1	25	94		3.3	70529	66297		-1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	99.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.1	24.89	64040	59538	4502	100	0.22957	0.22957	0.22667	0.26871	RANDOM	41.795

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]
1.48		5.39	-2.15		1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.321
r_dihedral_angle_4_deg	20.573
r_dihedral_angle_3_deg	15.325
r_dihedral_angle_1_deg	6.125
r_scangle_it	5.62
r_scbond_it	4.615
r_mcangle_it	3.312
r_mcbond_it	2.594
r_mcbond_other	1.689
r_angle_refined_deg	1.62
r_angle_other_deg	1.099
r_chiral_restr	0.094
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8386
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms

Software

Software
Software Name	Purpose
CBASS	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling