2FOL

Crystal structure of human RAB1A in complex with GDP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	25% PEG3350, 0.2M magnesium chloride, 0.1M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.79	α = 90
b = 75.79	β = 90
c = 49.08	γ = 120

Symmetry
Space Group	P 32 2 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	IMAGE PLATE	RIGAKU RAXIS IV++		2006-01-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

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	2.62	30	100	0.088		10.6		5102

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	2.62	2.71		100	0.826		10.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	pdb entries 1YZN, 1UKV	2.631	30	5048	233	99.98	0.201	0.199	0.2523	36.747

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]
-0.603	-0.302		-0.603		0.905

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.02
r_dihedral_angle_4_deg	24.925
r_dihedral_angle_3_deg	16.052
r_dihedral_angle_1_deg	4.754
r_scangle_it	1.662
r_angle_refined_deg	1.397
r_scbond_it	0.99
r_angle_other_deg	0.797
r_scangle_other	0.753
r_mcangle_it	0.599
r_mcbond_it	0.459
r_scbond_other	0.287
r_symmetry_vdw_other	0.277
r_mcangle_other	0.268
r_symmetry_hbond_refined	0.227
r_nbd_refined	0.223
r_nbd_other	0.209
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.19
r_symmetry_vdw_refined	0.167
r_metal_ion_refined	0.137
r_nbtor_other	0.097
r_chiral_restr	0.075
r_mcbond_other	0.069
r_bond_refined_d	0.019
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1240
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	31

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction