2F9M | pdb_00002f9m

3D structure of active human Rab11b GTPase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	reservoir solution: 0.1M Tris-HCl pH8.5, 1M lithium sulfate, 0.01M nickel chloride. Protein sample: 68 mg/ml Rab11b-GppNHp, 10mM Tris-HCl pH7.4, 0.1mM magnesium chloride., VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.611	α = 90
b = 85.409	β = 90
c = 86.886	γ = 90

Symmetry
Space Group	I 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	MARRESEARCH		2004-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.43	LNLS	D03B-MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	33.48	99.8	0.09	19.3	9.2		18222

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.95	2.06	100		0.331	6.6	9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.95	30	18438	17437	940	99.65	0.16479	0.16479	0.16263	0.1642	0.20529	0.157	RANDOM	17.688

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]
-0.66			-0.59		1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.324
r_dihedral_angle_3_deg	14.483
r_dihedral_angle_4_deg	13.887
r_dihedral_angle_1_deg	5.57
r_scangle_it	2.926
r_scbond_it	1.763
r_angle_refined_deg	1.263
r_mcangle_it	1.036
r_mcbond_it	0.56
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.225
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.149
r_symmetry_hbond_refined	0.135
r_chiral_restr	0.092
r_metal_ion_refined	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1456
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing