2GIL | pdb_00002gil

Structure of the extremely slow GTPase Rab6A in the GTP bound form at 1.8 resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D5C	PDB entry 1D5C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	100mM TrisHCl, 1M LiCl, 32% (w/v) polyethylene glycol 1000, 3.3mM Nonyl-D-glucoside, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.008	α = 90
b = 124.853	β = 107.57
c = 66.162	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.0398	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.82	19.05	87.7	0.056	0.032	17.44	1.9	48538	48538			25.99

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.82	1.9	52.2		0.249	0.146	4.3		3482

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	PDB entry 1D5C	1.82	19.05	46121	46121	2428	100	0.20849	0.20849	0.20484	0.21	0.27735	0.28	RANDOM	26.728

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.997
r_dihedral_angle_4_deg	20.478
r_dihedral_angle_3_deg	15.831
r_dihedral_angle_1_deg	5.799
r_scangle_it	2.835
r_scbond_it	1.894
r_angle_refined_deg	1.4
r_mcangle_it	1.343
r_mcbond_it	0.814
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.997
r_dihedral_angle_4_deg	20.478
r_dihedral_angle_3_deg	15.831
r_dihedral_angle_1_deg	5.799
r_scangle_it	2.835
r_scbond_it	1.894
r_angle_refined_deg	1.4
r_mcangle_it	1.343
r_mcbond_it	0.814
r_nbtor_refined	0.306
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.204
r_symmetry_hbond_refined	0.19
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.088
r_metal_ion_refined	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5194
Nucleic Acid Atoms
Solvent Atoms	739
Heterogen Atoms	132

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.