2FOL | pdb_00002fol

Crystal structure of human RAB1A in complex with GDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YZN	pdb entries 1YZN, 1UKV
experimental model	PDB	1UKV	pdb entries 1YZN, 1UKV

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	pdb entries 1YZN, 1UKV	2.631	30	5048	233	99.98	0.201	0.199	0.24	0.2523	0.23	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