2GF9

Crystal structure of human RAB3D 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	3RAB	pdb entry 3RAB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	20% PEG8000, 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.5, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.9	30.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.7	α = 90
b = 63.222	β = 90
c = 67.695	γ = 90

Symmetry
Space Group	P 21 21 21

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		2006-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	1.53	28.25	88.3	0.035	32.8	7.4		21079

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)
	1.53	1.58		28	0.056		1.8

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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	pdb entry 3RAB	1.53	28.25	21035	1069	88.349	0.155	0.1533	0.1854	random	8.16

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]
-0.293			0.166		0.127

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.992
r_dihedral_angle_4_deg	11.515
r_dihedral_angle_3_deg	11.213
r_dihedral_angle_1_deg	5.382
r_scangle_it	3.251
r_mcangle_it	2.418
r_scbond_it	2.183
r_mcbond_it	1.756
r_angle_refined_deg	1.344
r_angle_other_deg	0.874
r_mcbond_other	0.454
r_symmetry_vdw_other	0.333
r_nbd_refined	0.213
r_nbd_other	0.193
r_nbtor_refined	0.181
r_symmetry_hbond_refined	0.127
r_symmetry_vdw_refined	0.12
r_xyhbond_nbd_refined	0.116
r_nbtor_other	0.085
r_chiral_restr	0.078
r_bond_refined_d	0.015
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1438
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	31

Software

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