2F9L | pdb_00002f9l

3D structure of inactive human Rab11b GTPase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OIV	PDB ENTRY 1OIV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.8	298	Reservoir solution: 0.1M Tris-HCl pH8.8, 30% PEG 4000 Protein sample: 30 mg/ml Rab11b-GDP, 10mM Tris-HCl pH7.4, 0.1mM Mg Chloride , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.6	22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.79	α = 90
b = 52.218	β = 90
c = 59.351	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	MARRESEARCH		2003-08-30	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	1.55	39.22	99.8	0.062	18.4	6.7		21134

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)
	1.55	1.63	99.5		0.377	5	6.4

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 (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1OIV	1.55	39.22	21252	20119	1091	99.77	0.18813	0.18813	0.18564	0.23755	0.1923	RANDOM	18.203

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]
-0.34			-0.7		1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.806
r_dihedral_angle_4_deg	23.694
r_dihedral_angle_3_deg	16.101
r_dihedral_angle_1_deg	5.909
r_scangle_it	3.464
r_scbond_it	2.4
r_angle_refined_deg	1.72
r_mcangle_it	1.631
r_mcbond_it	0.975
r_nbtor_refined	0.332
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.211
r_symmetry_hbond_refined	0.19
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1341
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	29

Software

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