4HL4 | pdb_00004hl4

Crystal structure of the human TBC1D20 RabGAP domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	277	0.1M sodium acetate pH 4.5, 0.8M di-potassium hydrogen phospate, 0.8M sodium dihydrogen phosphate, 0.025M beryllium fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.55	α = 90
b = 73.55	β = 90
c = 113	γ = 120

Symmetry
Space Group	P 31 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	PIXEL	PSI PILATUS 6M		2011-10-09	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	PSI PILATUS 6M		2011-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9793	SLS	X10SA
2	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
1,2	2.2	50	99.9			18695	18508		-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)
1,2	2.2	2.3	99.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	SAD	THROUGHOUT	2.2	42.27	-3	18508	17582	926	100	0.20425	0.20259	0.2088	0.23489	0.24	RANDOM	64.211

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]
3.34	1.67		3.34		-5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.732
r_dihedral_angle_4_deg	26.61
r_dihedral_angle_3_deg	17.948
r_dihedral_angle_1_deg	6.542
r_scangle_it	4.883
r_scbond_it	3.144
r_mcangle_it	2.032
r_angle_refined_deg	1.867
r_mcbond_it	1.142
r_chiral_restr	0.123
r_bond_refined_d	0.022
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2220
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	12

Software

Software
Software Name	Purpose
XDS	data scaling
SOLVE	phasing
REFMAC	refinement
XDS	data reduction