1YZK

GppNHp bound Rab11 GTPase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Polyalanine Rab5c

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	NaCl, Glycerol, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.946	α = 90
b = 73.946	β = 90
c = 148.197	γ = 90

Symmetry
Space Group	I 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 300 mm plate		2003-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	2	50	99.8	0.058	31.6	7		14293			34.1

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)
	2	2.06	99.8		0.252	7.6	7	1139

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Polyalanine Rab5c	2	6	14295	12992	697	99.81	0.197	0.18006	0.17753	0.22829	RANDOM	22.315

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]
-0.3			-0.3		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.01
r_dihedral_angle_4_deg	13.849
r_dihedral_angle_3_deg	11.381
r_dihedral_angle_1_deg	5.213
r_scangle_it	1.782
r_scbond_it	1.196
r_angle_refined_deg	1.067
r_angle_other_deg	0.723
r_mcangle_it	0.723
r_mcbond_it	0.686
r_symmetry_vdw_other	0.294
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.188
r_nbtor_refined	0.174
r_nbd_other	0.17
r_xyhbond_nbd_refined	0.155
r_symmetry_vdw_refined	0.139
r_mcbond_other	0.081
r_nbtor_other	0.077
r_metal_ion_refined	0.062
r_chiral_restr	0.056
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1309
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing