3JZA

Crystal structure of human Rab1b in complex with the GEF domain of DrrA/SidM from Legionella pneumophila

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.75	292	0.1 M Sodium citrate, 35% v/v PEG 600, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.756	α = 90
b = 100.756	β = 90
c = 146.36	γ = 120

Symmetry
Space Group	P 63 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	CCD	MARMOSAIC 225 mm CCD		2008-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000000	SLS	X10SA

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	1.8	30	98.1	0.09	21.97			40529		-3	33.85

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)
1	1.8	1.9	97.1		0.456	4.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.8	29.63	40517	2005	98.13	0.202	0.201	0.234	RANDOM	17.349

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]
-2.79	-1.4		-2.79		4.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.354
r_dihedral_angle_4_deg	15.583
r_dihedral_angle_3_deg	14.364
r_dihedral_angle_1_deg	6.405
r_scangle_it	4.731
r_scbond_it	3.123
r_mcangle_it	2.067
r_angle_refined_deg	1.829
r_mcbond_it	1.292
r_angle_other_deg	1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.354
r_dihedral_angle_4_deg	15.583
r_dihedral_angle_3_deg	14.364
r_dihedral_angle_1_deg	6.405
r_scangle_it	4.731
r_scbond_it	3.123
r_mcangle_it	2.067
r_angle_refined_deg	1.829
r_mcbond_it	1.292
r_angle_other_deg	1.05
r_mcbond_other	0.464
r_chiral_restr	0.123
r_bond_refined_d	0.024
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2818
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	5

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.