2GZD | pdb_00002gzd

Crystal Structure of Rab11 in Complex with Rab11-FIP2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Rab11 in complex with Rab11-FIP in the trigonal space group

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5	298	Ammonium phosphate buffer, between 0.1 and 0.5 M concentration, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.364	α = 90
b = 91.149	β = 90
c = 113.099	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	MAR CCD 165 mm		2005-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97865	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.44	50	99.72	0.102	8.8	13	24131	24064	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.44	2.53	98.5		0.421		10	2565

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Rab11 in complex with Rab11-FIP in the trigonal space group	2.44	50	25403	24064	1290	99.72	0.22886	0.22886	0.22628	0.2274	0.27888	0.277	RANDOM	39.23

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]
-3.45			0.58		2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.282
r_dihedral_angle_4_deg	23.053
r_dihedral_angle_3_deg	19.594
r_dihedral_angle_1_deg	9.512
r_scangle_it	3.732
r_scbond_it	2.488
r_angle_refined_deg	1.974
r_mcangle_it	1.857
r_mcbond_it	1.154
r_symmetry_hbond_refined	0.313
r_nbtor_refined	0.304
r_nbd_refined	0.24
r_xyhbond_nbd_refined	0.191
r_symmetry_vdw_refined	0.145
r_chiral_restr	0.134
r_metal_ion_refined	0.049
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3258
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
AMoRE	phasing